Dear Marius, thanks again for the help. I'm trying to install blast_rbh (owner is peterjc). The dependencies look as follows: blast_rbh - biopython - package_biopython_1_64 - package_numpy_1_8 - package_atlas_3_10 - blast - package_blast_plus_2_2_31 - blast+ With unchecked "When available, install Tool Shed managed tool dependencies?" I get all as "Installed, missing tool dependencies". Blast_rbh is not working since blast+ is not installed. Even if I install blast+ manually (in galaxy) its not working (makeblastdb is missing). When I leave "When available, install Tool Shed managed tool dependencies?" I see blast_rbh, package_blast_plus package_biopython as installed and the others as Installed, missing tool dependencies. Here blast_rbh is working. What would be your suggestion? Live with the latter and file an issue at the tools repository (difficult to say which causes the problem(s))? I get similar behavior if I try to install from the test toolshed. (Only a different error from atlas: /bin/sh: line 3: /host/static_full_blas_lapack.diff: No such file or directory). But, actually I'm trying to automatize tool installation using the ansible role ansible-galaxy-tools (https://github.com/galaxyproject/ansible-galaxy-tools). With this method I get the latter behavior. The role uses uses ephemeris==0.4.0 to install tools. There I have seen three global variables that (I guess) control the installation of dependencies. INSTALL_TOOL_DEPENDENCIES = False INSTALL_REPOSITORY_DEPENDENCIES = True INSTALL_RESOLVER_DEPENDENCIES = True I guess I could control the behavior with the latter two variables. Best, Matthias On 18.04.2017 19:24, Marius van den Beek wrote:

Hi Matthias,

it's me again! What tool are you trying to install?

My -perhaps- unhelpful suggestion is to not install anything that starts with package_* (also called tool shed packages), those should be exclusively installed when you absolutely need to install an old tool that can only function with packages. We've switched to conda nowadays, which is much easier to install and to maintain. In fact the IUC has ported all their latest tools to conda, and similarly most devteam tools that are still in active use have also been ported to use Conda dependencies.

If you look at this document https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/, there is a part where you confirm dependencies. If you click on show detail, and you unselect When available, install Tool Shed managed tool dependencies? Galaxy will not try to install these old packages. There are some tools which come both with old toolshed dependencies and that have Conda available. You may be lucky and find that the tool you are trying to install has Conda dependencies available. There is a lot more background on the Toolshed and Conda in this document here: https://docs.galaxyproject.org/en/master/admin/conda_faq.html

Best, Marius

On 18 April 2017 at 19:03, Matthias Bernt <m.bernt@ufz.de <mailto:m.bernt@ufz.de>> wrote:

Dear list,

again me :( stumbling from problem to problem ...

I got compilation errors when installing

package_atlas_3_10 Revision: 98c017ec230d

I tried with gcc 4x and 6x without success. Do I need the intel C compiler for this tool?

If I got earlier posts (http://dev.list.galaxyproject.org/atlas-3-10-IUC-error-tt4668236.html <http://dev.list.galaxyproject.org/atlas-3-10-IUC-error-tt4668236.html>) correct a precompiled version should be used anyway?

I'm running galaxy on CentOS 6.8 (64bit) (running in a VirtualBox).

Best, Matthias

Here is the output (which I guess is verbose output from configure):

/tmp/cctyMGAH.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' probe_OS.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' probe_asm.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' system(make IRun_GAS_x8632 args="-v 2" MYFLAGS="-DATL_OS_Linux" 2> /dev/null | fgrep SUCCESS)

ierr=256 in command='make IRun_GAS_x8632 args="-v 2" MYFLAGS="-DATL_OS_Linux" 2> /dev/null | fgrep SUCCESS'!

OUTPUT: ======= system(make IRun_GAS_x8664 args="-v 2" MYFLAGS="-DATL_OS_Linux" 2> /dev/null | fgrep SUCCESS) probe_vec.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp'

ierr=256 in command='make IRun_VSX MYFLAGS='-DATL_OS_Linux -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!

OUTPUT: =======

ierr=256 in command='make IRun_AltiVec MYFLAGS='-DATL_OS_Linux -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!

OUTPUT: =======

ierr=256 in command='make IRun_AVXFMA4 MYFLAGS='-DATL_OS_Linux -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!

OUTPUT: =======

ierr=256 in command='make IRun_3DNow MYFLAGS='-DATL_OS_Linux -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!

OUTPUT: =======

ierr=256 in command='make IRun_NEON MYFLAGS='-DATL_OS_Linux -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!

OUTPUT: ======= probe_arch.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' /tmp/cc8hbxc1.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' ERROR: enum fam=3, chip=2, model=79, mach=0 make[3]: *** [atlas_run] Error 44 make[2]: *** [IRunArchInfo_x86] Error 2 /tmp/ccafA8Bi.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' ERROR: enum fam=3, chip=2, model=79, mach=0 make[3]: *** [atlas_run] Error 44 make[2]: *** [IRunArchInfo_x86] Error 2 ERROR: enum fam=3, chip=2, model=79, mach=0 make[3]: *** [atlas_run] Error 44 make[2]: *** [IRunArchInfo_x86] Error 2 cmnd='make IRun_comp args="-v 2 -o atlconf.txt -O 1 -A 39 -Si nof77 0 -V 488 -Fa ic '-fPIC' -Fa sm '-fPIC' -Fa dm '-fPIC' -Fa sk '-fPIC' -Fa dk '-fPIC' -Fa xc '-fPIC' -Fa gc '-fPIC' -Fa if '-fPIC' -b 64"' /tmp/cc8W8Itx.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' probe_comp.o: In function `ATL_tmpnam': /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp'

ierr=256 in command='find /gpfs1/data/galaxy_server/galaxy-dev/.venv/bin /usr/local/gcc/6.2.0-1/bin /global/apps/bioinf/galaxy/bin/Python-2.7.13/bin /usr/local/sqlite/3.15.1-1/bin /global/apps/bioinf/galaxy/bin/postgresql-9.6.2/bin /usr/local/git/2.10.1-1/bin /usr/local/pcre/8.38-1/bin /usr/local/ncurses/5.9-1/bin /usr/local/bzip2/1.0.6-3/bin /usr/local/expat/2.1.1-1/bin /usr/local/curl/7.41.0-1/bin /usr/local/openssl/1.0.2-1/usr/bin /usr/local/uge/8.4.4-1/bin/lx-amd64 /usr/local/bin /bin /usr/bin /usr/local/sbin /usr/sbin /sbin /home/songalax/bin -maxdepth 1 -name '*gcc*' -exec ./xisgcc '{}' \;'!

OUTPUT: ======= cmnd=make IRunCComp CC='/usr/local/gcc/6.2.0-1/bin/gcc' CCFLAGS='-O' | fgrep SUCCESS /usr/local/gcc/6.2.0-1/bin/gcc -O : SUCCESS! cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O' | fgrep SUCCESS /usr/bin/gcc -O : SUCCESS! sh: -c: line 0: unexpected EOF while looking for matching ``' sh: -c: line 1: syntax error: unexpected end of file

ierr=256 in command='find $HOME/local -name '*gcc*' -exec ./xisgcc '{}' \;'!

OUTPUT: ======= cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O' | fgrep SUCCESS /usr/bin/gcc -O : SUCCESS! sh: -c: line 0: unexpected EOF while looking for matching ``' sh: -c: line 1: syntax error: unexpected end of file

ierr=256 in command='find /usr/local /bin /sbin /usr/bin /usr/sbin /opt/bin /opt/sbin -name '*gcc*' -exec ./xisgcc '{}' \;'!

OUTPUT: ======= cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O' | fgrep SUCCESS /usr/bin/gcc -O : SUCCESS! sh: -c: line 0: unexpected EOF while looking for matching ``' sh: -c: line 1: syntax error: unexpected end of file sh: -c: line 0: unexpected EOF while looking for matching ``' sh: -c: line 1: syntax error: unexpected end of file

Compiler nodes: Fresh Read 0. priority=0, comps,OS,arch[0]=(128,1,1), comp='f77' '-O' 1. priority=4, comps,OS,arch[0]=(128,1,1), comp='g77' '-O' 2. priority=5, comps,OS,arch[0]=(128,1,1), comp='gfortran' '-O' 3. priority=5, comps,OS,arch[0]=(127,1,1), comp='gcc' '-O -fomit-frame-pointer' 4. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran' '-mcpu=cortex-a8 -mfpu=vfpv3 -mfloat-abi=softfp -O' 5. priority=1000, comps,OS,arch[0]=(20,1,0), comp='gcc' '-O1 -mcpu=cortex-a8 -mtune=cortex-a8 -mfpu=vfpv3 -mfloat-abi=softfp -fno-schedule-insns2' 6. priority=1000, comps,OS,arch[0]=(75,1,0), comp='gcc' '-O1 -mcpu=cortex-a8 -mtune=cortex-a8 -mfpu=vfpv3 -mfloat-abi=softfp -fno-expensive-optimizations' 7. priority=1000, comps,OS,arch[0]=(32,1,0), comp='gcc' '-mcpu=cortex-a8 -O1 -mfpu=vfpv3 -mfloat-abi=softfp ' 8. priority=0, comps,OS,arch[0]=(63,768,1075838976), comp='icl' '-QxN -O3 -Qprec -fp:extended -fp:except -nologo -Oy' 9. priority=0, comps,OS,arch[0]=(128,768,1), comp='ifort' '-O2 -fltconsistency -nologo' 10. priority=0, comps,OS,arch[0]=(63,768,1), comp='cl' '-Oy -Ox -arch:SSE2 -nologo' 11. priority=4, comps,OS,arch[0]=(63,768,1048576), comp='cl' '-Oy -Ox -arch:SSE -nologo' 12. priority=4, comps,OS,arch[0]=(63,768,983040), comp='cl' '-Oy -Ox' 13. priority=500, comps,OS,arch[0]=(127,1,3584), comp='gcc' '-O3 -funroll-loops' 14. priority=500, comps,OS,arch[0]=(128,1,3584), comp='gfortran' '-O3 -funroll-loops' 15. priority=600, comps,OS,arch[0]=(128,1,2048), comp='gfortran' '-march=z9-109 -O3 -funroll-loops' 16. priority=600, comps,OS,arch[0]=(127,1,2048), comp='gcc' '-march=z9-109 -O3 -funroll-loops' 17. priority=800, comps,OS,arch[0]=(128,1,2048), comp='gfortran' '-march=z10 -O3 -funroll-loops -fno-prefetch-loop-arrays' 18. priority=800, comps,OS,arch[0]=(127,1,2048), comp='gcc' '-march=z10 -O3 -funroll-loops -fno-prefetch-loop-arrays' 19. priority=1000, comps,OS,arch[0]=(127,1,2048), comp='gcc' '-march=z196 -O3 -funroll-loops -fno-prefetch-loop-arrays' 20. priority=1000, comps,OS,arch[0]=(128,1,2048), comp='gfortran' '-march=z196 -O3 -funroll-loops -fno-prefetch-loop-arrays' 21. priority=600, comps,OS,arch[0]=(127,1,1024), comp='gcc' '-march=z9-109 -O3 -funroll-loops -fno-prefetch-loop-arrays' 22. priority=600, comps,OS,arch[0]=(128,1,1024), comp='gfortran' '-march=z9-109 -O3 -funroll-loops' 23. priority=1000, comps,OS,arch[0]=(127,1,1024), comp='gcc' '-march=z10 -O3 -funroll-loops -fno-prefetch-loop-arrays' 24. priority=1000, comps,OS,arch[0]=(127,1,512), comp='gcc' '-march=z9-109 -O3 -funroll-loops' 25. priority=1010, comps,OS,arch[0]=(128,1,4), comp='xlf' '-qtune=pwr4 -qarch=pwr4 -O3 -qmaxmem=-1 -qfloat=hsflt' 26. priority=1010, comps,OS,arch[0]=(127,1,4), comp='gcc' '-mcpu=power4 -mtune=power4 -O3 -fno-schedule-insns -fno-rerun-loop-opt' 27. priority=1010, comps,OS,arch[0]=(128,1,8), comp='xlf' '-qtune=pwr5 -qarch=pwr5 -O3 -qmaxmem=-1 -qfloat=hsflt' 28. priority=1010, comps,OS,arch[0]=(128,1,128), comp='xlf' '-qtune=pwr7 -qarch=pwr7 -O3 -qmaxmem=-1 -qfloat=hsflt' 29. priority=1010, comps,OS,arch[0]=(128,1,8), comp='gfortran' '-mcpu=power5 -mtune=power5 -O3 -fno-schedule-insns -fno-rerun-loop-opt' 30. priority=1010, comps,OS,arch[0]=(128,1,64), comp='gfortran' '-mcpu=power6 -mtune=power6 -maltivec -O3 -fno-schedule-insns -fschedule-insns2 -minsert-sched-nops=2' 31. priority=1010, comps,OS,arch[0]=(127,1,8), comp='gcc' '-mcpu=power5 -mtune=power5 -O3 -fno-schedule-insns -fno-rerun-loop-opt' 32. priority=1010, comps,OS,arch[0]=(127,1,64), comp='gcc' '-mcpu=power6 -mtune=power6 -maltivec -O3 -fno-schedule-insns -fschedule-insns2 -minsert-sched-nops=2' 33. priority=1010, comps,OS,arch[0]=(128,1,128), comp='gfortran' '-O2 -mvsx -mcpu=power7 -mtune=power7 -m64 -mvrsave -funroll-all-loops' 34. priority=1010, comps,OS,arch[0]=(127,1,128), comp='gcc' '-O2 -mvsx -mcpu=power7 -mtune=power7 -m64 -mvrsave -funroll-all-loops' 35. priority=1000, comps,OS,arch[0]=(8,1,32), comp='gcc' '-mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970 -O2 -mvrsave' 36. priority=1000, comps,OS,arch[0]=(117,1,32), comp='gcc' '-mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970 -O2' 37. priority=1000, comps,OS,arch[0]=(2,1,32), comp='gcc' '-Os -mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970 -mvrsave -fno-schedule-insns2 -fno-schedule-insns' 38. priority=1000, comps,OS,arch[0]=(121,1,16), comp='gcc' '-O3 -maltivec -mabi=altivec -mcpu=7400 -mtune=7400 -fno-schedule-insns -fschedule-insns2' 39. priority=1000, comps,OS,arch[0]=(2,1,16), comp='gcc' '-Os -maltivec -mabi=altivec -mcpu=7400 -mtune=7400' 40. priority=1000, comps,OS,arch[0]=(4,1,16), comp='gcc' '-Os -maltivec -mabi=altivec -mcpu=7400 -mtune=7400' 41. priority=1, comps,OS,arch[0]=(33,1,0), comp='pathcc' '-march=auto -O2 -OPT:Olimit=15000 -LNO:blocking=OFF' 42. priority=1, comps,OS,arch[0]=(6,1,0), comp='pathcc' '-O3 -OPT:Olimit=15000 -LNO:blocking=OFF -LOPT:alias=typed -march=auto -LNO:opt=0 -LNO:full_unroll_outer=OFF -LNO:fusion=0 -LNO:prefetch=2' 43. priority=1, comps,OS,arch[0]=(24,1,0), comp='pathcc' '-O3 -OPT:Olimit=15000 -LNO:blocking=OFF -LOPT:alias=typed -march=auto' 44. priority=1000, comps,OS,arch[0]=(128,1,0), comp='pathf95' '-march=auto -O2' 45. priority=500, comps,OS,arch[0]=(127,1,0), comp='gcc' '-O2 -mips64 -march=5kf -mtune=5kf -fno-schedule-insns -fschedule-insns2 -fno-peephole -fno-peephole2' 46. priority=1000, comps,OS,arch[0]=(128,32,0), comp='f77' '-O2' 47. priority=1000, comps,OS,arch[0]=(97,32,0), comp='cc' '-O2 -OPT:Olimit=15000 -LNO:blocking=OFF' 48. priority=1000, comps,OS,arch[0]=(30,32,0), comp='cc' '-O3 -OPT:Olimit=15000 -LNO:blocking=OFF -LOPT:alias=typed' 49. priority=1010, comps,OS,arch[0]=(128,1,0), comp='gfortran' '-fomit-frame-pointer -O2 -fno-tree-loop-optimize' 50. priority=1000, comps,OS,arch[0]=(30,1,0), comp='gcc' '-fomit-frame-pointer -O2' 51. priority=1010, comps,OS,arch[0]=(30,1,0), comp='gcc' '-fomit-frame-pointer -O2 -fno-tree-loop-optimize' 52. priority=10, comps,OS,arch[0]=(128,1,0), comp='g77' '-O -mcpu=ultrasparc3 -mtune=ultrasparc3' 53. priority=100, comps,OS,arch[0]=(128,1,0), comp='gfortran' '-O -mcpu=ultrasparc3 -mtune=ultrasparc3' 54. priority=1000, comps,OS,arch[0]=(128,1,0), comp='f77' '-dalign -native -xO5' 55. priority=1000, comps,OS,arch[0]=(96,1,0), comp='gcc' '-mcpu=ultrasparc3 -mtune=ultrasparc3 -O' 56. priority=1000, comps,OS,arch[0]=(29,1,0), comp='gcc' '-O3 -mcpu=ultrasparc3 -mtune=ultrasparc3 -fno-schedule-insns2 -fschedule-insns' 57. priority=1000, comps,OS,arch[0]=(2,1,0), comp='gcc' '-O1 -mcpu=ultrasparc3 -mtune=ultrasparc3 -fschedule-insns -fmodulo-sched' 58. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran' '-mcpu=niagara2 -mtune=niagara2 -Os' 59. priority=1000, comps,OS,arch[0]=(127,1,0), comp='gcc' '-mcpu=niagara2 -mtune=niagara2 -Os' 60. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -mfma4 -O2 -fno-tree-loop-optimize' 61. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc' '-Os -fomit-frame-pointer' 62. priority=1005, comps,OS,arch[0]=(95,896,0), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 63. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 64. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran' '-fomit-frame-pointer -mfpmath=sse -O2' 65. priority=1000, comps,OS,arch[0]=(95,1,12582912), comp='gcc' '-fomit-frame-pointer -O3 -mfpmath=387' 66. priority=1005, comps,OS,arch[0]=(31,896,12582912), comp='gcc-4' '-fomit-frame-pointer -O3 -mfpmath=387' 67. priority=1000, comps,OS,arch[0]=(95,1,-1071906816), comp='gcc' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 68. priority=1005, comps,OS,arch[0]=(31,896,1835008), comp='gcc-4' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 69. priority=1000, comps,OS,arch[0]=(128,1,1835008), comp='gfortran' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 70. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc' '-fomit-frame-pointer -mfpmath=387 -O2' 71. priority=1005, comps,OS,arch[0]=(31,896,0), comp='gcc-4' '-fomit-frame-pointer -mfpmath=387 -O2' 72. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran' '-fomit-frame-pointer -mfpmath=387 -O2' 73. priority=1000, comps,OS,arch[0]=(25,1,-1073741824), comp='gcc-4' '-O2 -fomit-frame-pointer -mfpmath=sse' 74. priority=1005, comps,OS,arch[0]=(6,896,-1073741824), comp='gcc-4' '-O2 -fomit-frame-pointer -mfpmath=sse -fno-schedule-insns -fno-optimize-register-move' 75. priority=1000, comps,OS,arch[0]=(6,1,-1073741824), comp='gcc' '-O2 -fomit-frame-pointer -mfpmath=sse -fno-schedule-insns -fno-optimize-register-move' 76. priority=1000, comps,OS,arch[0]=(25,1,-2147483648), comp='gcc' '-O2 -fomit-frame-pointer -mfpmath=sse' 77. priority=1000, comps,OS,arch[0]=(128,1,-1073741824), comp='gfortran' '-O2 -fomit-frame-pointer -mfpmath=sse' 78. priority=1000, comps,OS,arch[0]=(128,1,32768), comp='gfortran' '-fomit-frame-pointer -mfpmath=sse -O2' 79. priority=1000, comps,OS,arch[0]=(95,1,32768), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 80. priority=1000, comps,OS,arch[0]=(128,1,16384), comp='gfortran' '-fomit-frame-pointer -mfpmath=sse -O2' 81. priority=1000, comps,OS,arch[0]=(95,1,16384), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 82. priority=1000, comps,OS,arch[0]=(128,1,8192), comp='gfortran' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 83. priority=1000, comps,OS,arch[0]=(10,1,8192), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 84. priority=1000, comps,OS,arch[0]=(85,1,8192), comp='gcc' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 85. priority=1000, comps,OS,arch[0]=(128,1,12288), comp='gfortran' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 86. priority=1000, comps,OS,arch[0]=(95,1,4096), comp='gcc' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 87. priority=1000, comps,OS,arch[0]=(65,1,536870912), comp='gcc' '-O' 88. priority=1000, comps,OS,arch[0]=(30,1,536870912), comp='gcc' '-O3 -fno-schedule-insns2 -funroll-all-loops -fno-tree-ch' 89. priority=1000, comps,OS,arch[0]=(95,1,33554432), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 90. priority=1005, comps,OS,arch[0]=(31,896,33554432), comp='gcc-4' '-fomit-frame-pointer -mfpmath=sse -O2' 91. priority=1000, comps,OS,arch[0]=(95,1,67108864), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2' 92. priority=1005, comps,OS,arch[0]=(95,896,67108864), comp='gcc-4' '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2' 93. priority=50, comps,OS,arch[0]=(57,1,134217728), comp='clang' '-fomit-frame-pointer -mavx -O2 -m64 -Wno-parentheses' 94. priority=1000, comps,OS,arch[0]=(127,1,134217728), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2' 95. priority=1005, comps,OS,arch[0]=(31,896,134217728), comp='gcc-4' '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2' 96. priority=1000, comps,OS,arch[0]=(127,1,268435456), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2'

Compiler nodes: Targeted 0. priority=0, comps,OS,arch[0]=(128,1,1), comp='f77' '-O' 1. priority=4, comps,OS,arch[0]=(128,1,1), comp='g77' '-O' 2. priority=5, comps,OS,arch[0]=(128,1,1), comp='gfortran' '-O' 3. priority=5, comps,OS,arch[0]=(127,1,1), comp='gcc' '-O -fomit-frame-pointer'

Compiler nodes: Sorted 0. priority=0, comps,OS,arch[0]=(128,1,1), comp='f77' '-O' 1. priority=4, comps,OS,arch[0]=(128,1,1), comp='g77' '-O' 2. priority=5, comps,OS,arch[0]=(127,1,1), comp='gcc' '-O -fomit-frame-pointer' 3. priority=5, comps,OS,arch[0]=(128,1,1), comp='gfortran' '-O'

cc1: error: unrecognized command line option "-mavx2" make[2]: *** [IRunCComp] Error 1

ierr=256 in command='make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O -fomit-frame-pointer -mavx2 -mfma -fPIC -m64' | fgrep SUCCESS'!

OUTPUT: ======= cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O -fomit-frame-pointer -mavx2 -mfma -fPIC -m64' | fgrep SUCCESS /usr/bin/gcc -O -fomit-frame-pointer -mavx2 -mfma -fPIC -m64 : FAILURE!

Unable to find usable compiler for ICC; abortingMake sure compilers are in your path, and specify good compilers to configure (see INSTALL.txt or 'configure --help' for details)make[1]: *** [atlas_run] Error 1 make: *** [IRun_comp] Error 2 ERROR 512 IN SYSCMND: 'make IRun_comp args="-v 2 -o atlconf.txt -O 1 -A 39 -Si nof77 0 -V 488 -Fa ic '-fPIC' -Fa sm '-fPIC' -Fa dm '-fPIC' -Fa sk '-fPIC' -Fa dk '-fPIC' -Fa xc '-fPIC' -Fa gc '-fPIC' -Fa if '-fPIC' -b 64"' Make.top:1: Make.inc: No such file or directory Make.top:329: warning: overriding commands for target `/AtlasTest' Make.top:80: warning: ignoring old commands for target `/AtlasTest' make[1]: *** No rule to make target `Make.inc'. Stop. make: *** [startup] Error 2 mv: cannot stat `lib/Makefile': No such file or directory ../configure: line 450: lib/Makefile: No such file or directory ../configure: line 451: lib/Makefile: No such file or directory ../configure: line 452: lib/Makefile: No such file or directory ../configure: line 453: lib/Makefile: No such file or directory ../configure: line 509: lib/Makefile: No such file or directory Make.top:1: Make.inc: No such file or directory Make.top:329: warning: overriding commands for target `/AtlasTest' Make.top:80: warning: ignoring old commands for target `/AtlasTest' make[1]: *** No rule to make target `Make.inc'. Stop. make: *** [build] Error 2 --

------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296 <tel:%2B49%20341%20235%20482296>, m.bernt@ufz.de <mailto:m.bernt@ufz.de>, www.ufz.de <http://www.ufz.de>

Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

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-- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

Dear Peter, thanks for the info. Would be great to get the update, but since I have a method that is working for the moment there is no need to hurry. Best, Matthias On 19.04.2017 12:57, Peter Cock wrote:

Oh right - I've just been updating ncbi_blast_plus this morning to transition to BLAST+ 2.5.0 via either bioconda or the older legacy Tool Shed.

I can try to update blast_rbh next, which may solve this by letting you use bioconda.

Peter

On Wed, Apr 19, 2017 at 11:52 AM, Matthias Bernt <m.bernt@ufz.de> wrote:

...

Dear Marius,

thanks again for the help. I'm trying to install blast_rbh (owner is peterjc). The dependencies look as follows:

blast_rbh - biopython - package_biopython_1_64 - package_numpy_1_8 - package_atlas_3_10 - blast - package_blast_plus_2_2_31 - blast+

With unchecked "When available, install Tool Shed managed tool dependencies?" I get all as "Installed, missing tool dependencies". Blast_rbh is not working since blast+ is not installed. Even if I install blast+ manually (in galaxy) its not working (makeblastdb is missing).

When I leave "When available, install Tool Shed managed tool dependencies?" I see blast_rbh, package_blast_plus package_biopython as installed and the others as Installed, missing tool dependencies. Here blast_rbh is working.

What would be your suggestion? Live with the latter and file an issue at the tools repository (difficult to say which causes the problem(s))?

I get similar behavior if I try to install from the test toolshed. (Only a different error from atlas: /bin/sh: line 3: /host/static_full_blas_lapack.diff: No such file or directory).

But, actually I'm trying to automatize tool installation using the ansible role ansible-galaxy-tools (https://github.com/galaxyproject/ansible-galaxy-tools). With this method I get the latter behavior. The role uses uses ephemeris==0.4.0 to install tools. There I have seen three global variables that (I guess) control the installation of dependencies.

INSTALL_TOOL_DEPENDENCIES = False INSTALL_REPOSITORY_DEPENDENCIES = True INSTALL_RESOLVER_DEPENDENCIES = True

I guess I could control the behavior with the latter two variables.

Best, Matthias

On 18.04.2017 19:24, Marius van den Beek wrote:

...

Hi Matthias,

it's me again! What tool are you trying to install?

My -perhaps- unhelpful suggestion is to not install anything that starts with package_* (also called tool shed packages), those should be exclusively installed when you absolutely need to install an old tool that can only function with packages. We've switched to conda nowadays, which is much easier to install and to maintain. In fact the IUC has ported all their latest tools to conda, and similarly most devteam tools that are still in active use have also been ported to use Conda dependencies.

If you look at this document https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/, there is a part where you confirm dependencies. If you click on show detail, and you unselect When available, install Tool Shed managed tool dependencies? Galaxy will not try to install these old packages. There are some tools which come both with old toolshed dependencies and that have Conda available. You may be lucky and find that the tool you are trying to install has Conda dependencies available. There is a lot more background on the Toolshed and Conda in this document here: https://docs.galaxyproject.org/en/master/admin/conda_faq.html

Best, Marius

On 18 April 2017 at 19:03, Matthias Bernt <m.bernt@ufz.de <mailto:m.bernt@ufz.de>> wrote:

Dear list,

again me :( stumbling from problem to problem ...

I got compilation errors when installing

package_atlas_3_10 Revision: 98c017ec230d

I tried with gcc 4x and 6x without success. Do I need the intel C compiler for this tool?

If I got earlier posts (http://dev.list.galaxyproject.org/atlas-3-10-IUC-error-tt4668236.html

<http://dev.list.galaxyproject.org/atlas-3-10-IUC-error-tt4668236.html>)

correct a precompiled version should be used anyway?

I'm running galaxy on CentOS 6.8 (64bit) (running in a VirtualBox).

Best, Matthias

Here is the output (which I guess is verbose output from configure):

/tmp/cctyMGAH.o: In function `ATL_tmpnam':

/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' probe_OS.o: In function `ATL_tmpnam':

/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' probe_asm.o: In function `ATL_tmpnam':

/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' system(make IRun_GAS_x8632 args="-v 2" MYFLAGS="-DATL_OS_Linux" 2> /dev/null | fgrep SUCCESS)

ierr=256 in command='make IRun_GAS_x8632 args="-v 2" MYFLAGS="-DATL_OS_Linux" 2> /dev/null | fgrep SUCCESS'!

OUTPUT: ======= system(make IRun_GAS_x8664 args="-v 2" MYFLAGS="-DATL_OS_Linux" 2> /dev/null | fgrep SUCCESS) probe_vec.o: In function `ATL_tmpnam':

/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp'

ierr=256 in command='make IRun_VSX MYFLAGS='-DATL_OS_Linux -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!

OUTPUT: =======

ierr=256 in command='make IRun_AltiVec MYFLAGS='-DATL_OS_Linux -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!

OUTPUT: =======

ierr=256 in command='make IRun_AVXFMA4 MYFLAGS='-DATL_OS_Linux -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!

OUTPUT: =======

ierr=256 in command='make IRun_3DNow MYFLAGS='-DATL_OS_Linux -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!

OUTPUT: =======

ierr=256 in command='make IRun_NEON MYFLAGS='-DATL_OS_Linux -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!

OUTPUT: ======= probe_arch.o: In function `ATL_tmpnam':

/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' /tmp/cc8hbxc1.o: In function `ATL_tmpnam':

/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' ERROR: enum fam=3, chip=2, model=79, mach=0 make[3]: *** [atlas_run] Error 44 make[2]: *** [IRunArchInfo_x86] Error 2 /tmp/ccafA8Bi.o: In function `ATL_tmpnam':

/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' ERROR: enum fam=3, chip=2, model=79, mach=0 make[3]: *** [atlas_run] Error 44 make[2]: *** [IRunArchInfo_x86] Error 2 ERROR: enum fam=3, chip=2, model=79, mach=0 make[3]: *** [atlas_run] Error 44 make[2]: *** [IRunArchInfo_x86] Error 2 cmnd='make IRun_comp args="-v 2 -o atlconf.txt -O 1 -A 39 -Si nof77 0 -V 488 -Fa ic '-fPIC' -Fa sm '-fPIC' -Fa dm '-fPIC' -Fa sk '-fPIC' -Fa dk '-fPIC' -Fa xc '-fPIC' -Fa gc '-fPIC' -Fa if '-fPIC' -b 64"' /tmp/cc8W8Itx.o: In function `ATL_tmpnam':

/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' probe_comp.o: In function `ATL_tmpnam':

/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp'

ierr=256 in command='find /gpfs1/data/galaxy_server/galaxy-dev/.venv/bin /usr/local/gcc/6.2.0-1/bin /global/apps/bioinf/galaxy/bin/Python-2.7.13/bin /usr/local/sqlite/3.15.1-1/bin /global/apps/bioinf/galaxy/bin/postgresql-9.6.2/bin /usr/local/git/2.10.1-1/bin /usr/local/pcre/8.38-1/bin /usr/local/ncurses/5.9-1/bin /usr/local/bzip2/1.0.6-3/bin /usr/local/expat/2.1.1-1/bin /usr/local/curl/7.41.0-1/bin /usr/local/openssl/1.0.2-1/usr/bin /usr/local/uge/8.4.4-1/bin/lx-amd64 /usr/local/bin /bin /usr/bin /usr/local/sbin /usr/sbin /sbin /home/songalax/bin -maxdepth 1 -name '*gcc*' -exec ./xisgcc '{}' \;'!

OUTPUT: ======= cmnd=make IRunCComp CC='/usr/local/gcc/6.2.0-1/bin/gcc' CCFLAGS='-O' | fgrep SUCCESS /usr/local/gcc/6.2.0-1/bin/gcc -O : SUCCESS! cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O' | fgrep SUCCESS /usr/bin/gcc -O : SUCCESS! sh: -c: line 0: unexpected EOF while looking for matching ``' sh: -c: line 1: syntax error: unexpected end of file

ierr=256 in command='find $HOME/local -name '*gcc*' -exec ./xisgcc '{}' \;'!

OUTPUT: ======= cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O' | fgrep SUCCESS /usr/bin/gcc -O : SUCCESS! sh: -c: line 0: unexpected EOF while looking for matching ``' sh: -c: line 1: syntax error: unexpected end of file

ierr=256 in command='find /usr/local /bin /sbin /usr/bin /usr/sbin /opt/bin /opt/sbin -name '*gcc*' -exec ./xisgcc '{}' \;'!

OUTPUT: ======= cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O' | fgrep SUCCESS /usr/bin/gcc -O : SUCCESS! sh: -c: line 0: unexpected EOF while looking for matching ``' sh: -c: line 1: syntax error: unexpected end of file sh: -c: line 0: unexpected EOF while looking for matching ``' sh: -c: line 1: syntax error: unexpected end of file

Compiler nodes: Fresh Read 0. priority=0, comps,OS,arch[0]=(128,1,1), comp='f77' '-O' 1. priority=4, comps,OS,arch[0]=(128,1,1), comp='g77' '-O' 2. priority=5, comps,OS,arch[0]=(128,1,1), comp='gfortran' '-O' 3. priority=5, comps,OS,arch[0]=(127,1,1), comp='gcc' '-O -fomit-frame-pointer' 4. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran' '-mcpu=cortex-a8 -mfpu=vfpv3 -mfloat-abi=softfp -O' 5. priority=1000, comps,OS,arch[0]=(20,1,0), comp='gcc' '-O1 -mcpu=cortex-a8 -mtune=cortex-a8 -mfpu=vfpv3 -mfloat-abi=softfp -fno-schedule-insns2' 6. priority=1000, comps,OS,arch[0]=(75,1,0), comp='gcc' '-O1 -mcpu=cortex-a8 -mtune=cortex-a8 -mfpu=vfpv3 -mfloat-abi=softfp -fno-expensive-optimizations' 7. priority=1000, comps,OS,arch[0]=(32,1,0), comp='gcc' '-mcpu=cortex-a8 -O1 -mfpu=vfpv3 -mfloat-abi=softfp ' 8. priority=0, comps,OS,arch[0]=(63,768,1075838976), comp='icl' '-QxN -O3 -Qprec -fp:extended -fp:except -nologo -Oy' 9. priority=0, comps,OS,arch[0]=(128,768,1), comp='ifort' '-O2 -fltconsistency -nologo' 10. priority=0, comps,OS,arch[0]=(63,768,1), comp='cl' '-Oy -Ox -arch:SSE2 -nologo' 11. priority=4, comps,OS,arch[0]=(63,768,1048576), comp='cl' '-Oy -Ox -arch:SSE -nologo' 12. priority=4, comps,OS,arch[0]=(63,768,983040), comp='cl' '-Oy -Ox' 13. priority=500, comps,OS,arch[0]=(127,1,3584), comp='gcc' '-O3 -funroll-loops' 14. priority=500, comps,OS,arch[0]=(128,1,3584), comp='gfortran' '-O3 -funroll-loops' 15. priority=600, comps,OS,arch[0]=(128,1,2048), comp='gfortran' '-march=z9-109 -O3 -funroll-loops' 16. priority=600, comps,OS,arch[0]=(127,1,2048), comp='gcc' '-march=z9-109 -O3 -funroll-loops' 17. priority=800, comps,OS,arch[0]=(128,1,2048), comp='gfortran' '-march=z10 -O3 -funroll-loops -fno-prefetch-loop-arrays' 18. priority=800, comps,OS,arch[0]=(127,1,2048), comp='gcc' '-march=z10 -O3 -funroll-loops -fno-prefetch-loop-arrays' 19. priority=1000, comps,OS,arch[0]=(127,1,2048), comp='gcc' '-march=z196 -O3 -funroll-loops -fno-prefetch-loop-arrays' 20. priority=1000, comps,OS,arch[0]=(128,1,2048), comp='gfortran' '-march=z196 -O3 -funroll-loops -fno-prefetch-loop-arrays' 21. priority=600, comps,OS,arch[0]=(127,1,1024), comp='gcc' '-march=z9-109 -O3 -funroll-loops -fno-prefetch-loop-arrays' 22. priority=600, comps,OS,arch[0]=(128,1,1024), comp='gfortran' '-march=z9-109 -O3 -funroll-loops' 23. priority=1000, comps,OS,arch[0]=(127,1,1024), comp='gcc' '-march=z10 -O3 -funroll-loops -fno-prefetch-loop-arrays' 24. priority=1000, comps,OS,arch[0]=(127,1,512), comp='gcc' '-march=z9-109 -O3 -funroll-loops' 25. priority=1010, comps,OS,arch[0]=(128,1,4), comp='xlf' '-qtune=pwr4 -qarch=pwr4 -O3 -qmaxmem=-1 -qfloat=hsflt' 26. priority=1010, comps,OS,arch[0]=(127,1,4), comp='gcc' '-mcpu=power4 -mtune=power4 -O3 -fno-schedule-insns -fno-rerun-loop-opt' 27. priority=1010, comps,OS,arch[0]=(128,1,8), comp='xlf' '-qtune=pwr5 -qarch=pwr5 -O3 -qmaxmem=-1 -qfloat=hsflt' 28. priority=1010, comps,OS,arch[0]=(128,1,128), comp='xlf' '-qtune=pwr7 -qarch=pwr7 -O3 -qmaxmem=-1 -qfloat=hsflt' 29. priority=1010, comps,OS,arch[0]=(128,1,8), comp='gfortran' '-mcpu=power5 -mtune=power5 -O3 -fno-schedule-insns -fno-rerun-loop-opt' 30. priority=1010, comps,OS,arch[0]=(128,1,64), comp='gfortran' '-mcpu=power6 -mtune=power6 -maltivec -O3 -fno-schedule-insns -fschedule-insns2 -minsert-sched-nops=2' 31. priority=1010, comps,OS,arch[0]=(127,1,8), comp='gcc' '-mcpu=power5 -mtune=power5 -O3 -fno-schedule-insns -fno-rerun-loop-opt' 32. priority=1010, comps,OS,arch[0]=(127,1,64), comp='gcc' '-mcpu=power6 -mtune=power6 -maltivec -O3 -fno-schedule-insns -fschedule-insns2 -minsert-sched-nops=2' 33. priority=1010, comps,OS,arch[0]=(128,1,128), comp='gfortran' '-O2 -mvsx -mcpu=power7 -mtune=power7 -m64 -mvrsave -funroll-all-loops' 34. priority=1010, comps,OS,arch[0]=(127,1,128), comp='gcc' '-O2 -mvsx -mcpu=power7 -mtune=power7 -m64 -mvrsave -funroll-all-loops' 35. priority=1000, comps,OS,arch[0]=(8,1,32), comp='gcc' '-mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970 -O2 -mvrsave' 36. priority=1000, comps,OS,arch[0]=(117,1,32), comp='gcc' '-mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970 -O2' 37. priority=1000, comps,OS,arch[0]=(2,1,32), comp='gcc' '-Os -mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970 -mvrsave -fno-schedule-insns2 -fno-schedule-insns' 38. priority=1000, comps,OS,arch[0]=(121,1,16), comp='gcc' '-O3 -maltivec -mabi=altivec -mcpu=7400 -mtune=7400 -fno-schedule-insns -fschedule-insns2' 39. priority=1000, comps,OS,arch[0]=(2,1,16), comp='gcc' '-Os -maltivec -mabi=altivec -mcpu=7400 -mtune=7400' 40. priority=1000, comps,OS,arch[0]=(4,1,16), comp='gcc' '-Os -maltivec -mabi=altivec -mcpu=7400 -mtune=7400' 41. priority=1, comps,OS,arch[0]=(33,1,0), comp='pathcc' '-march=auto -O2 -OPT:Olimit=15000 -LNO:blocking=OFF' 42. priority=1, comps,OS,arch[0]=(6,1,0), comp='pathcc' '-O3 -OPT:Olimit=15000 -LNO:blocking=OFF -LOPT:alias=typed -march=auto -LNO:opt=0 -LNO:full_unroll_outer=OFF -LNO:fusion=0 -LNO:prefetch=2' 43. priority=1, comps,OS,arch[0]=(24,1,0), comp='pathcc' '-O3 -OPT:Olimit=15000 -LNO:blocking=OFF -LOPT:alias=typed -march=auto' 44. priority=1000, comps,OS,arch[0]=(128,1,0), comp='pathf95' '-march=auto -O2' 45. priority=500, comps,OS,arch[0]=(127,1,0), comp='gcc' '-O2 -mips64 -march=5kf -mtune=5kf -fno-schedule-insns -fschedule-insns2 -fno-peephole -fno-peephole2' 46. priority=1000, comps,OS,arch[0]=(128,32,0), comp='f77' '-O2' 47. priority=1000, comps,OS,arch[0]=(97,32,0), comp='cc' '-O2 -OPT:Olimit=15000 -LNO:blocking=OFF' 48. priority=1000, comps,OS,arch[0]=(30,32,0), comp='cc' '-O3 -OPT:Olimit=15000 -LNO:blocking=OFF -LOPT:alias=typed' 49. priority=1010, comps,OS,arch[0]=(128,1,0), comp='gfortran' '-fomit-frame-pointer -O2 -fno-tree-loop-optimize' 50. priority=1000, comps,OS,arch[0]=(30,1,0), comp='gcc' '-fomit-frame-pointer -O2' 51. priority=1010, comps,OS,arch[0]=(30,1,0), comp='gcc' '-fomit-frame-pointer -O2 -fno-tree-loop-optimize' 52. priority=10, comps,OS,arch[0]=(128,1,0), comp='g77' '-O -mcpu=ultrasparc3 -mtune=ultrasparc3' 53. priority=100, comps,OS,arch[0]=(128,1,0), comp='gfortran' '-O -mcpu=ultrasparc3 -mtune=ultrasparc3' 54. priority=1000, comps,OS,arch[0]=(128,1,0), comp='f77' '-dalign -native -xO5' 55. priority=1000, comps,OS,arch[0]=(96,1,0), comp='gcc' '-mcpu=ultrasparc3 -mtune=ultrasparc3 -O' 56. priority=1000, comps,OS,arch[0]=(29,1,0), comp='gcc' '-O3 -mcpu=ultrasparc3 -mtune=ultrasparc3 -fno-schedule-insns2 -fschedule-insns' 57. priority=1000, comps,OS,arch[0]=(2,1,0), comp='gcc' '-O1 -mcpu=ultrasparc3 -mtune=ultrasparc3 -fschedule-insns -fmodulo-sched' 58. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran' '-mcpu=niagara2 -mtune=niagara2 -Os' 59. priority=1000, comps,OS,arch[0]=(127,1,0), comp='gcc' '-mcpu=niagara2 -mtune=niagara2 -Os' 60. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -mfma4 -O2 -fno-tree-loop-optimize' 61. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc' '-Os -fomit-frame-pointer' 62. priority=1005, comps,OS,arch[0]=(95,896,0), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 63. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 64. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran' '-fomit-frame-pointer -mfpmath=sse -O2' 65. priority=1000, comps,OS,arch[0]=(95,1,12582912), comp='gcc' '-fomit-frame-pointer -O3 -mfpmath=387' 66. priority=1005, comps,OS,arch[0]=(31,896,12582912), comp='gcc-4' '-fomit-frame-pointer -O3 -mfpmath=387' 67. priority=1000, comps,OS,arch[0]=(95,1,-1071906816), comp='gcc' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 68. priority=1005, comps,OS,arch[0]=(31,896,1835008), comp='gcc-4' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 69. priority=1000, comps,OS,arch[0]=(128,1,1835008), comp='gfortran' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 70. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc' '-fomit-frame-pointer -mfpmath=387 -O2' 71. priority=1005, comps,OS,arch[0]=(31,896,0), comp='gcc-4' '-fomit-frame-pointer -mfpmath=387 -O2' 72. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran' '-fomit-frame-pointer -mfpmath=387 -O2' 73. priority=1000, comps,OS,arch[0]=(25,1,-1073741824), comp='gcc-4' '-O2 -fomit-frame-pointer -mfpmath=sse' 74. priority=1005, comps,OS,arch[0]=(6,896,-1073741824), comp='gcc-4' '-O2 -fomit-frame-pointer -mfpmath=sse -fno-schedule-insns -fno-optimize-register-move' 75. priority=1000, comps,OS,arch[0]=(6,1,-1073741824), comp='gcc' '-O2 -fomit-frame-pointer -mfpmath=sse -fno-schedule-insns -fno-optimize-register-move' 76. priority=1000, comps,OS,arch[0]=(25,1,-2147483648), comp='gcc' '-O2 -fomit-frame-pointer -mfpmath=sse' 77. priority=1000, comps,OS,arch[0]=(128,1,-1073741824), comp='gfortran' '-O2 -fomit-frame-pointer -mfpmath=sse' 78. priority=1000, comps,OS,arch[0]=(128,1,32768), comp='gfortran' '-fomit-frame-pointer -mfpmath=sse -O2' 79. priority=1000, comps,OS,arch[0]=(95,1,32768), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 80. priority=1000, comps,OS,arch[0]=(128,1,16384), comp='gfortran' '-fomit-frame-pointer -mfpmath=sse -O2' 81. priority=1000, comps,OS,arch[0]=(95,1,16384), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 82. priority=1000, comps,OS,arch[0]=(128,1,8192), comp='gfortran' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 83. priority=1000, comps,OS,arch[0]=(10,1,8192), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 84. priority=1000, comps,OS,arch[0]=(85,1,8192), comp='gcc' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 85. priority=1000, comps,OS,arch[0]=(128,1,12288), comp='gfortran' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 86. priority=1000, comps,OS,arch[0]=(95,1,4096), comp='gcc' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 87. priority=1000, comps,OS,arch[0]=(65,1,536870912), comp='gcc' '-O' 88. priority=1000, comps,OS,arch[0]=(30,1,536870912), comp='gcc' '-O3 -fno-schedule-insns2 -funroll-all-loops -fno-tree-ch' 89. priority=1000, comps,OS,arch[0]=(95,1,33554432), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 90. priority=1005, comps,OS,arch[0]=(31,896,33554432), comp='gcc-4' '-fomit-frame-pointer -mfpmath=sse -O2' 91. priority=1000, comps,OS,arch[0]=(95,1,67108864), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2' 92. priority=1005, comps,OS,arch[0]=(95,896,67108864), comp='gcc-4' '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2' 93. priority=50, comps,OS,arch[0]=(57,1,134217728), comp='clang' '-fomit-frame-pointer -mavx -O2 -m64 -Wno-parentheses' 94. priority=1000, comps,OS,arch[0]=(127,1,134217728), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2' 95. priority=1005, comps,OS,arch[0]=(31,896,134217728), comp='gcc-4' '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2' 96. priority=1000, comps,OS,arch[0]=(127,1,268435456), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2'

Compiler nodes: Targeted 0. priority=0, comps,OS,arch[0]=(128,1,1), comp='f77' '-O' 1. priority=4, comps,OS,arch[0]=(128,1,1), comp='g77' '-O' 2. priority=5, comps,OS,arch[0]=(128,1,1), comp='gfortran' '-O' 3. priority=5, comps,OS,arch[0]=(127,1,1), comp='gcc' '-O -fomit-frame-pointer'

Compiler nodes: Sorted 0. priority=0, comps,OS,arch[0]=(128,1,1), comp='f77' '-O' 1. priority=4, comps,OS,arch[0]=(128,1,1), comp='g77' '-O' 2. priority=5, comps,OS,arch[0]=(127,1,1), comp='gcc' '-O -fomit-frame-pointer' 3. priority=5, comps,OS,arch[0]=(128,1,1), comp='gfortran' '-O'

cc1: error: unrecognized command line option "-mavx2" make[2]: *** [IRunCComp] Error 1

ierr=256 in command='make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O -fomit-frame-pointer -mavx2 -mfma -fPIC -m64' | fgrep SUCCESS'!

OUTPUT: ======= cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O -fomit-frame-pointer -mavx2 -mfma -fPIC -m64' | fgrep SUCCESS /usr/bin/gcc -O -fomit-frame-pointer -mavx2 -mfma -fPIC -m64 : FAILURE!

Unable to find usable compiler for ICC; abortingMake sure compilers are in your path, and specify good compilers to configure (see INSTALL.txt or 'configure --help' for details)make[1]: *** [atlas_run] Error 1 make: *** [IRun_comp] Error 2 ERROR 512 IN SYSCMND: 'make IRun_comp args="-v 2 -o atlconf.txt -O 1 -A 39 -Si nof77 0 -V 488 -Fa ic '-fPIC' -Fa sm '-fPIC' -Fa dm '-fPIC' -Fa sk '-fPIC' -Fa dk '-fPIC' -Fa xc '-fPIC' -Fa gc '-fPIC' -Fa if '-fPIC' -b 64"' Make.top:1: Make.inc: No such file or directory Make.top:329: warning: overriding commands for target `/AtlasTest' Make.top:80: warning: ignoring old commands for target `/AtlasTest' make[1]: *** No rule to make target `Make.inc'. Stop. make: *** [startup] Error 2 mv: cannot stat `lib/Makefile': No such file or directory ../configure: line 450: lib/Makefile: No such file or directory ../configure: line 451: lib/Makefile: No such file or directory ../configure: line 452: lib/Makefile: No such file or directory ../configure: line 453: lib/Makefile: No such file or directory ../configure: line 509: lib/Makefile: No such file or directory Make.top:1: Make.inc: No such file or directory Make.top:329: warning: overriding commands for target `/AtlasTest' Make.top:80: warning: ignoring old commands for target `/AtlasTest' make[1]: *** No rule to make target `Make.inc'. Stop. make: *** [build] Error 2 --

------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296 <tel:%2B49%20341%20235%20482296>, m.bernt@ufz.de <mailto:m.bernt@ufz.de>, www.ufz.de <http://www.ufz.de>

Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/>

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--

------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/

-- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

Dear Peter, thanks. Just for understanding: Why not just change the biopython dependency from 1.67 to 1.69, if this is the one available in bioconda. blast_rbh seems to use only the SeqIO fasta parser and writer. This should be no problem. But I guess that for older versions of blast_rbh one might still need legacy packages of biopython. Or could one change the dependencies in older versions? Or would this be no good idea because of backward compatibility? Cheers, Matthias On 19.04.2017 13:50, Peter Cock wrote:

Just lucky timing, could you try blast_rbh v0.1.11,

https://toolshed.g2.bx.psu.edu/view/peterjc/blast_rbh/d8d9a9069586

For BLAST+ this ought to work with either bioconda, or the legacy XML based packages, as both have BLAST+ 2.5.0.

However, it looks like bioconda only has Biopython 1.68 and 1.69, while the legacy XML based packages only go up to Biopython 1.67 at the time of writing... it looks like we'll need to add a couple more legacy packages.

Peter

On Wed, Apr 19, 2017 at 12:01 PM, Matthias Bernt <m.bernt@ufz.de> wrote:

...

Dear Peter,

thanks for the info. Would be great to get the update, but since I have a method that is working for the moment there is no need to hurry.

Best, Matthias

On 19.04.2017 12:57, Peter Cock wrote:

...

Oh right - I've just been updating ncbi_blast_plus this morning to transition to BLAST+ 2.5.0 via either bioconda or the older legacy Tool Shed.

I can try to update blast_rbh next, which may solve this by letting you use bioconda.

Peter

On Wed, Apr 19, 2017 at 11:52 AM, Matthias Bernt <m.bernt@ufz.de> wrote:

...

Dear Marius,

thanks again for the help. I'm trying to install blast_rbh (owner is peterjc). The dependencies look as follows:

blast_rbh - biopython - package_biopython_1_64 - package_numpy_1_8 - package_atlas_3_10 - blast - package_blast_plus_2_2_31 - blast+

With unchecked "When available, install Tool Shed managed tool dependencies?" I get all as "Installed, missing tool dependencies". Blast_rbh is not working since blast+ is not installed. Even if I install blast+ manually (in galaxy) its not working (makeblastdb is missing).

When I leave "When available, install Tool Shed managed tool dependencies?" I see blast_rbh, package_blast_plus package_biopython as installed and the others as Installed, missing tool dependencies. Here blast_rbh is working.

What would be your suggestion? Live with the latter and file an issue at the tools repository (difficult to say which causes the problem(s))?

I get similar behavior if I try to install from the test toolshed. (Only a different error from atlas: /bin/sh: line 3: /host/static_full_blas_lapack.diff: No such file or directory).

But, actually I'm trying to automatize tool installation using the ansible role ansible-galaxy-tools (https://github.com/galaxyproject/ansible-galaxy-tools). With this method I get the latter behavior. The role uses uses ephemeris==0.4.0 to install tools. There I have seen three global variables that (I guess) control the installation of dependencies.

INSTALL_TOOL_DEPENDENCIES = False INSTALL_REPOSITORY_DEPENDENCIES = True INSTALL_RESOLVER_DEPENDENCIES = True

I guess I could control the behavior with the latter two variables.

Best, Matthias

On 18.04.2017 19:24, Marius van den Beek wrote:

...

Hi Matthias,

it's me again! What tool are you trying to install?

My -perhaps- unhelpful suggestion is to not install anything that starts with package_* (also called tool shed packages), those should be exclusively installed when you absolutely need to install an old tool that can only function with packages. We've switched to conda nowadays, which is much easier to install and to maintain. In fact the IUC has ported all their latest tools to conda, and similarly most devteam tools that are still in active use have also been ported to use Conda dependencies.

If you look at this document https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/, there is a part where you confirm dependencies. If you click on show detail, and you unselect When available, install Tool Shed managed tool dependencies? Galaxy will not try to install these old packages. There are some tools which come both with old toolshed dependencies and that have Conda available. You may be lucky and find that the tool you are trying to install has Conda dependencies available. There is a lot more background on the Toolshed and Conda in this document here: https://docs.galaxyproject.org/en/master/admin/conda_faq.html

Best, Marius

On 18 April 2017 at 19:03, Matthias Bernt <m.bernt@ufz.de <mailto:m.bernt@ufz.de>> wrote:

Dear list,

again me :( stumbling from problem to problem ...

I got compilation errors when installing

package_atlas_3_10 Revision: 98c017ec230d

I tried with gcc 4x and 6x without success. Do I need the intel C compiler for this tool?

If I got earlier posts

(http://dev.list.galaxyproject.org/atlas-3-10-IUC-error-tt4668236.html

<http://dev.list.galaxyproject.org/atlas-3-10-IUC-error-tt4668236.html>)

correct a precompiled version should be used anyway?

I'm running galaxy on CentOS 6.8 (64bit) (running in a VirtualBox).

Best, Matthias

Here is the output (which I guess is verbose output from configure):

/tmp/cctyMGAH.o: In function `ATL_tmpnam':

/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' probe_OS.o: In function `ATL_tmpnam':

/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' probe_asm.o: In function `ATL_tmpnam':

/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' system(make IRun_GAS_x8632 args="-v 2" MYFLAGS="-DATL_OS_Linux" 2> /dev/null | fgrep SUCCESS)

ierr=256 in command='make IRun_GAS_x8632 args="-v 2" MYFLAGS="-DATL_OS_Linux" 2> /dev/null | fgrep SUCCESS'!

OUTPUT: ======= system(make IRun_GAS_x8664 args="-v 2" MYFLAGS="-DATL_OS_Linux" 2> /dev/null | fgrep SUCCESS) probe_vec.o: In function `ATL_tmpnam':

/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp'

ierr=256 in command='make IRun_VSX MYFLAGS='-DATL_OS_Linux -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!

OUTPUT: =======

ierr=256 in command='make IRun_AltiVec MYFLAGS='-DATL_OS_Linux -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!

OUTPUT: =======

ierr=256 in command='make IRun_AVXFMA4 MYFLAGS='-DATL_OS_Linux -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!

OUTPUT: =======

ierr=256 in command='make IRun_3DNow MYFLAGS='-DATL_OS_Linux -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!

OUTPUT: =======

ierr=256 in command='make IRun_NEON MYFLAGS='-DATL_OS_Linux -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'!

OUTPUT: ======= probe_arch.o: In function `ATL_tmpnam':

/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' /tmp/cc8hbxc1.o: In function `ATL_tmpnam':

/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' ERROR: enum fam=3, chip=2, model=79, mach=0 make[3]: *** [atlas_run] Error 44 make[2]: *** [IRunArchInfo_x86] Error 2 /tmp/ccafA8Bi.o: In function `ATL_tmpnam':

/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' ERROR: enum fam=3, chip=2, model=79, mach=0 make[3]: *** [atlas_run] Error 44 make[2]: *** [IRunArchInfo_x86] Error 2 ERROR: enum fam=3, chip=2, model=79, mach=0 make[3]: *** [atlas_run] Error 44 make[2]: *** [IRunArchInfo_x86] Error 2 cmnd='make IRun_comp args="-v 2 -o atlconf.txt -O 1 -A 39 -Si nof77 0 -V 488 -Fa ic '-fPIC' -Fa sm '-fPIC' -Fa dm '-fPIC' -Fa sk '-fPIC' -Fa dk '-fPIC' -Fa xc '-fPIC' -Fa gc '-fPIC' -Fa if '-fPIC' -b 64"' /tmp/cc8W8Itx.o: In function `ATL_tmpnam':

/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp' probe_comp.o: In function `ATL_tmpnam':

/gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: warning: the use of `tmpnam' is dangerous, better use `mkstemp'

ierr=256 in command='find /gpfs1/data/galaxy_server/galaxy-dev/.venv/bin /usr/local/gcc/6.2.0-1/bin /global/apps/bioinf/galaxy/bin/Python-2.7.13/bin /usr/local/sqlite/3.15.1-1/bin /global/apps/bioinf/galaxy/bin/postgresql-9.6.2/bin /usr/local/git/2.10.1-1/bin /usr/local/pcre/8.38-1/bin /usr/local/ncurses/5.9-1/bin /usr/local/bzip2/1.0.6-3/bin /usr/local/expat/2.1.1-1/bin /usr/local/curl/7.41.0-1/bin /usr/local/openssl/1.0.2-1/usr/bin /usr/local/uge/8.4.4-1/bin/lx-amd64 /usr/local/bin /bin /usr/bin /usr/local/sbin /usr/sbin /sbin /home/songalax/bin -maxdepth 1 -name '*gcc*' -exec ./xisgcc '{}' \;'!

OUTPUT: ======= cmnd=make IRunCComp CC='/usr/local/gcc/6.2.0-1/bin/gcc' CCFLAGS='-O' | fgrep SUCCESS /usr/local/gcc/6.2.0-1/bin/gcc -O : SUCCESS! cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O' | fgrep SUCCESS /usr/bin/gcc -O : SUCCESS! sh: -c: line 0: unexpected EOF while looking for matching ``' sh: -c: line 1: syntax error: unexpected end of file

ierr=256 in command='find $HOME/local -name '*gcc*' -exec ./xisgcc '{}' \;'!

OUTPUT: ======= cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O' | fgrep SUCCESS /usr/bin/gcc -O : SUCCESS! sh: -c: line 0: unexpected EOF while looking for matching ``' sh: -c: line 1: syntax error: unexpected end of file

ierr=256 in command='find /usr/local /bin /sbin /usr/bin /usr/sbin /opt/bin /opt/sbin -name '*gcc*' -exec ./xisgcc '{}' \;'!

OUTPUT: ======= cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O' | fgrep SUCCESS /usr/bin/gcc -O : SUCCESS! sh: -c: line 0: unexpected EOF while looking for matching ``' sh: -c: line 1: syntax error: unexpected end of file sh: -c: line 0: unexpected EOF while looking for matching ``' sh: -c: line 1: syntax error: unexpected end of file

Compiler nodes: Fresh Read 0. priority=0, comps,OS,arch[0]=(128,1,1), comp='f77' '-O' 1. priority=4, comps,OS,arch[0]=(128,1,1), comp='g77' '-O' 2. priority=5, comps,OS,arch[0]=(128,1,1), comp='gfortran' '-O' 3. priority=5, comps,OS,arch[0]=(127,1,1), comp='gcc' '-O -fomit-frame-pointer' 4. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran' '-mcpu=cortex-a8 -mfpu=vfpv3 -mfloat-abi=softfp -O' 5. priority=1000, comps,OS,arch[0]=(20,1,0), comp='gcc' '-O1 -mcpu=cortex-a8 -mtune=cortex-a8 -mfpu=vfpv3 -mfloat-abi=softfp -fno-schedule-insns2' 6. priority=1000, comps,OS,arch[0]=(75,1,0), comp='gcc' '-O1 -mcpu=cortex-a8 -mtune=cortex-a8 -mfpu=vfpv3 -mfloat-abi=softfp -fno-expensive-optimizations' 7. priority=1000, comps,OS,arch[0]=(32,1,0), comp='gcc' '-mcpu=cortex-a8 -O1 -mfpu=vfpv3 -mfloat-abi=softfp ' 8. priority=0, comps,OS,arch[0]=(63,768,1075838976), comp='icl' '-QxN -O3 -Qprec -fp:extended -fp:except -nologo -Oy' 9. priority=0, comps,OS,arch[0]=(128,768,1), comp='ifort' '-O2 -fltconsistency -nologo' 10. priority=0, comps,OS,arch[0]=(63,768,1), comp='cl' '-Oy -Ox -arch:SSE2 -nologo' 11. priority=4, comps,OS,arch[0]=(63,768,1048576), comp='cl' '-Oy -Ox -arch:SSE -nologo' 12. priority=4, comps,OS,arch[0]=(63,768,983040), comp='cl' '-Oy -Ox' 13. priority=500, comps,OS,arch[0]=(127,1,3584), comp='gcc' '-O3 -funroll-loops' 14. priority=500, comps,OS,arch[0]=(128,1,3584), comp='gfortran' '-O3 -funroll-loops' 15. priority=600, comps,OS,arch[0]=(128,1,2048), comp='gfortran' '-march=z9-109 -O3 -funroll-loops' 16. priority=600, comps,OS,arch[0]=(127,1,2048), comp='gcc' '-march=z9-109 -O3 -funroll-loops' 17. priority=800, comps,OS,arch[0]=(128,1,2048), comp='gfortran' '-march=z10 -O3 -funroll-loops -fno-prefetch-loop-arrays' 18. priority=800, comps,OS,arch[0]=(127,1,2048), comp='gcc' '-march=z10 -O3 -funroll-loops -fno-prefetch-loop-arrays' 19. priority=1000, comps,OS,arch[0]=(127,1,2048), comp='gcc' '-march=z196 -O3 -funroll-loops -fno-prefetch-loop-arrays' 20. priority=1000, comps,OS,arch[0]=(128,1,2048), comp='gfortran' '-march=z196 -O3 -funroll-loops -fno-prefetch-loop-arrays' 21. priority=600, comps,OS,arch[0]=(127,1,1024), comp='gcc' '-march=z9-109 -O3 -funroll-loops -fno-prefetch-loop-arrays' 22. priority=600, comps,OS,arch[0]=(128,1,1024), comp='gfortran' '-march=z9-109 -O3 -funroll-loops' 23. priority=1000, comps,OS,arch[0]=(127,1,1024), comp='gcc' '-march=z10 -O3 -funroll-loops -fno-prefetch-loop-arrays' 24. priority=1000, comps,OS,arch[0]=(127,1,512), comp='gcc' '-march=z9-109 -O3 -funroll-loops' 25. priority=1010, comps,OS,arch[0]=(128,1,4), comp='xlf' '-qtune=pwr4 -qarch=pwr4 -O3 -qmaxmem=-1 -qfloat=hsflt' 26. priority=1010, comps,OS,arch[0]=(127,1,4), comp='gcc' '-mcpu=power4 -mtune=power4 -O3 -fno-schedule-insns -fno-rerun-loop-opt' 27. priority=1010, comps,OS,arch[0]=(128,1,8), comp='xlf' '-qtune=pwr5 -qarch=pwr5 -O3 -qmaxmem=-1 -qfloat=hsflt' 28. priority=1010, comps,OS,arch[0]=(128,1,128), comp='xlf' '-qtune=pwr7 -qarch=pwr7 -O3 -qmaxmem=-1 -qfloat=hsflt' 29. priority=1010, comps,OS,arch[0]=(128,1,8), comp='gfortran' '-mcpu=power5 -mtune=power5 -O3 -fno-schedule-insns -fno-rerun-loop-opt' 30. priority=1010, comps,OS,arch[0]=(128,1,64), comp='gfortran' '-mcpu=power6 -mtune=power6 -maltivec -O3 -fno-schedule-insns -fschedule-insns2 -minsert-sched-nops=2' 31. priority=1010, comps,OS,arch[0]=(127,1,8), comp='gcc' '-mcpu=power5 -mtune=power5 -O3 -fno-schedule-insns -fno-rerun-loop-opt' 32. priority=1010, comps,OS,arch[0]=(127,1,64), comp='gcc' '-mcpu=power6 -mtune=power6 -maltivec -O3 -fno-schedule-insns -fschedule-insns2 -minsert-sched-nops=2' 33. priority=1010, comps,OS,arch[0]=(128,1,128), comp='gfortran' '-O2 -mvsx -mcpu=power7 -mtune=power7 -m64 -mvrsave -funroll-all-loops' 34. priority=1010, comps,OS,arch[0]=(127,1,128), comp='gcc' '-O2 -mvsx -mcpu=power7 -mtune=power7 -m64 -mvrsave -funroll-all-loops' 35. priority=1000, comps,OS,arch[0]=(8,1,32), comp='gcc' '-mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970 -O2 -mvrsave' 36. priority=1000, comps,OS,arch[0]=(117,1,32), comp='gcc' '-mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970 -O2' 37. priority=1000, comps,OS,arch[0]=(2,1,32), comp='gcc' '-Os -mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970 -mvrsave -fno-schedule-insns2 -fno-schedule-insns' 38. priority=1000, comps,OS,arch[0]=(121,1,16), comp='gcc' '-O3 -maltivec -mabi=altivec -mcpu=7400 -mtune=7400 -fno-schedule-insns -fschedule-insns2' 39. priority=1000, comps,OS,arch[0]=(2,1,16), comp='gcc' '-Os -maltivec -mabi=altivec -mcpu=7400 -mtune=7400' 40. priority=1000, comps,OS,arch[0]=(4,1,16), comp='gcc' '-Os -maltivec -mabi=altivec -mcpu=7400 -mtune=7400' 41. priority=1, comps,OS,arch[0]=(33,1,0), comp='pathcc' '-march=auto -O2 -OPT:Olimit=15000 -LNO:blocking=OFF' 42. priority=1, comps,OS,arch[0]=(6,1,0), comp='pathcc' '-O3 -OPT:Olimit=15000 -LNO:blocking=OFF -LOPT:alias=typed -march=auto -LNO:opt=0 -LNO:full_unroll_outer=OFF -LNO:fusion=0 -LNO:prefetch=2' 43. priority=1, comps,OS,arch[0]=(24,1,0), comp='pathcc' '-O3 -OPT:Olimit=15000 -LNO:blocking=OFF -LOPT:alias=typed -march=auto' 44. priority=1000, comps,OS,arch[0]=(128,1,0), comp='pathf95' '-march=auto -O2' 45. priority=500, comps,OS,arch[0]=(127,1,0), comp='gcc' '-O2 -mips64 -march=5kf -mtune=5kf -fno-schedule-insns -fschedule-insns2 -fno-peephole -fno-peephole2' 46. priority=1000, comps,OS,arch[0]=(128,32,0), comp='f77' '-O2' 47. priority=1000, comps,OS,arch[0]=(97,32,0), comp='cc' '-O2 -OPT:Olimit=15000 -LNO:blocking=OFF' 48. priority=1000, comps,OS,arch[0]=(30,32,0), comp='cc' '-O3 -OPT:Olimit=15000 -LNO:blocking=OFF -LOPT:alias=typed' 49. priority=1010, comps,OS,arch[0]=(128,1,0), comp='gfortran' '-fomit-frame-pointer -O2 -fno-tree-loop-optimize' 50. priority=1000, comps,OS,arch[0]=(30,1,0), comp='gcc' '-fomit-frame-pointer -O2' 51. priority=1010, comps,OS,arch[0]=(30,1,0), comp='gcc' '-fomit-frame-pointer -O2 -fno-tree-loop-optimize' 52. priority=10, comps,OS,arch[0]=(128,1,0), comp='g77' '-O -mcpu=ultrasparc3 -mtune=ultrasparc3' 53. priority=100, comps,OS,arch[0]=(128,1,0), comp='gfortran' '-O -mcpu=ultrasparc3 -mtune=ultrasparc3' 54. priority=1000, comps,OS,arch[0]=(128,1,0), comp='f77' '-dalign -native -xO5' 55. priority=1000, comps,OS,arch[0]=(96,1,0), comp='gcc' '-mcpu=ultrasparc3 -mtune=ultrasparc3 -O' 56. priority=1000, comps,OS,arch[0]=(29,1,0), comp='gcc' '-O3 -mcpu=ultrasparc3 -mtune=ultrasparc3 -fno-schedule-insns2 -fschedule-insns' 57. priority=1000, comps,OS,arch[0]=(2,1,0), comp='gcc' '-O1 -mcpu=ultrasparc3 -mtune=ultrasparc3 -fschedule-insns -fmodulo-sched' 58. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran' '-mcpu=niagara2 -mtune=niagara2 -Os' 59. priority=1000, comps,OS,arch[0]=(127,1,0), comp='gcc' '-mcpu=niagara2 -mtune=niagara2 -Os' 60. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -mfma4 -O2 -fno-tree-loop-optimize' 61. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc' '-Os -fomit-frame-pointer' 62. priority=1005, comps,OS,arch[0]=(95,896,0), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 63. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 64. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran' '-fomit-frame-pointer -mfpmath=sse -O2' 65. priority=1000, comps,OS,arch[0]=(95,1,12582912), comp='gcc' '-fomit-frame-pointer -O3 -mfpmath=387' 66. priority=1005, comps,OS,arch[0]=(31,896,12582912), comp='gcc-4' '-fomit-frame-pointer -O3 -mfpmath=387' 67. priority=1000, comps,OS,arch[0]=(95,1,-1071906816), comp='gcc' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 68. priority=1005, comps,OS,arch[0]=(31,896,1835008), comp='gcc-4' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 69. priority=1000, comps,OS,arch[0]=(128,1,1835008), comp='gfortran' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 70. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc' '-fomit-frame-pointer -mfpmath=387 -O2' 71. priority=1005, comps,OS,arch[0]=(31,896,0), comp='gcc-4' '-fomit-frame-pointer -mfpmath=387 -O2' 72. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran' '-fomit-frame-pointer -mfpmath=387 -O2' 73. priority=1000, comps,OS,arch[0]=(25,1,-1073741824), comp='gcc-4' '-O2 -fomit-frame-pointer -mfpmath=sse' 74. priority=1005, comps,OS,arch[0]=(6,896,-1073741824), comp='gcc-4' '-O2 -fomit-frame-pointer -mfpmath=sse -fno-schedule-insns -fno-optimize-register-move' 75. priority=1000, comps,OS,arch[0]=(6,1,-1073741824), comp='gcc' '-O2 -fomit-frame-pointer -mfpmath=sse -fno-schedule-insns -fno-optimize-register-move' 76. priority=1000, comps,OS,arch[0]=(25,1,-2147483648), comp='gcc' '-O2 -fomit-frame-pointer -mfpmath=sse' 77. priority=1000, comps,OS,arch[0]=(128,1,-1073741824), comp='gfortran' '-O2 -fomit-frame-pointer -mfpmath=sse' 78. priority=1000, comps,OS,arch[0]=(128,1,32768), comp='gfortran' '-fomit-frame-pointer -mfpmath=sse -O2' 79. priority=1000, comps,OS,arch[0]=(95,1,32768), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 80. priority=1000, comps,OS,arch[0]=(128,1,16384), comp='gfortran' '-fomit-frame-pointer -mfpmath=sse -O2' 81. priority=1000, comps,OS,arch[0]=(95,1,16384), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 82. priority=1000, comps,OS,arch[0]=(128,1,8192), comp='gfortran' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 83. priority=1000, comps,OS,arch[0]=(10,1,8192), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 84. priority=1000, comps,OS,arch[0]=(85,1,8192), comp='gcc' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 85. priority=1000, comps,OS,arch[0]=(128,1,12288), comp='gfortran' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 86. priority=1000, comps,OS,arch[0]=(95,1,4096), comp='gcc' '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' 87. priority=1000, comps,OS,arch[0]=(65,1,536870912), comp='gcc' '-O' 88. priority=1000, comps,OS,arch[0]=(30,1,536870912), comp='gcc' '-O3 -fno-schedule-insns2 -funroll-all-loops -fno-tree-ch' 89. priority=1000, comps,OS,arch[0]=(95,1,33554432), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2' 90. priority=1005, comps,OS,arch[0]=(31,896,33554432), comp='gcc-4' '-fomit-frame-pointer -mfpmath=sse -O2' 91. priority=1000, comps,OS,arch[0]=(95,1,67108864), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2' 92. priority=1005, comps,OS,arch[0]=(95,896,67108864), comp='gcc-4' '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2' 93. priority=50, comps,OS,arch[0]=(57,1,134217728), comp='clang' '-fomit-frame-pointer -mavx -O2 -m64 -Wno-parentheses' 94. priority=1000, comps,OS,arch[0]=(127,1,134217728), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2' 95. priority=1005, comps,OS,arch[0]=(31,896,134217728), comp='gcc-4' '-fomit-frame-pointer -mfpmath=sse -O2 -fno-schedule-insns2' 96. priority=1000, comps,OS,arch[0]=(127,1,268435456), comp='gcc' '-fomit-frame-pointer -mfpmath=sse -O2'

Compiler nodes: Targeted 0. priority=0, comps,OS,arch[0]=(128,1,1), comp='f77' '-O' 1. priority=4, comps,OS,arch[0]=(128,1,1), comp='g77' '-O' 2. priority=5, comps,OS,arch[0]=(128,1,1), comp='gfortran' '-O' 3. priority=5, comps,OS,arch[0]=(127,1,1), comp='gcc' '-O -fomit-frame-pointer'

Compiler nodes: Sorted 0. priority=0, comps,OS,arch[0]=(128,1,1), comp='f77' '-O' 1. priority=4, comps,OS,arch[0]=(128,1,1), comp='g77' '-O' 2. priority=5, comps,OS,arch[0]=(127,1,1), comp='gcc' '-O -fomit-frame-pointer' 3. priority=5, comps,OS,arch[0]=(128,1,1), comp='gfortran' '-O'

cc1: error: unrecognized command line option "-mavx2" make[2]: *** [IRunCComp] Error 1

ierr=256 in command='make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O -fomit-frame-pointer -mavx2 -mfma -fPIC -m64' | fgrep SUCCESS'!

OUTPUT: ======= cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O -fomit-frame-pointer -mavx2 -mfma -fPIC -m64' | fgrep SUCCESS /usr/bin/gcc -O -fomit-frame-pointer -mavx2 -mfma -fPIC -m64 : FAILURE!

Unable to find usable compiler for ICC; abortingMake sure compilers are in your path, and specify good compilers to configure (see INSTALL.txt or 'configure --help' for details)make[1]: *** [atlas_run] Error 1 make: *** [IRun_comp] Error 2 ERROR 512 IN SYSCMND: 'make IRun_comp args="-v 2 -o atlconf.txt -O 1 -A 39 -Si nof77 0 -V 488 -Fa ic '-fPIC' -Fa sm '-fPIC' -Fa dm '-fPIC' -Fa sk '-fPIC' -Fa dk '-fPIC' -Fa xc '-fPIC' -Fa gc '-fPIC' -Fa if '-fPIC' -b 64"' Make.top:1: Make.inc: No such file or directory Make.top:329: warning: overriding commands for target `/AtlasTest' Make.top:80: warning: ignoring old commands for target `/AtlasTest' make[1]: *** No rule to make target `Make.inc'. Stop. make: *** [startup] Error 2 mv: cannot stat `lib/Makefile': No such file or directory ../configure: line 450: lib/Makefile: No such file or directory ../configure: line 451: lib/Makefile: No such file or directory ../configure: line 452: lib/Makefile: No such file or directory ../configure: line 453: lib/Makefile: No such file or directory ../configure: line 509: lib/Makefile: No such file or directory Make.top:1: Make.inc: No such file or directory Make.top:329: warning: overriding commands for target `/AtlasTest' Make.top:80: warning: ignoring old commands for target `/AtlasTest' make[1]: *** No rule to make target `Make.inc'. Stop. make: *** [build] Error 2 --

------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296 <tel:%2B49%20341%20235%20482296>, m.bernt@ufz.de <mailto:m.bernt@ufz.de>, www.ufz.de <http://www.ufz.de>

Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/>

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/ <http://galaxyproject.org/search/>

--

------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/

--

------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

-- ------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

Good news: With Marius' help Biopython 1.67 should be in bioconda shortly, https://github.com/bioconda/bioconda-recipes/pull/4462 That means any Galaxy package using Biopython needing/wanting to work under both the legacy XML packaging system and bioconda will be able to point at Biopython 1.67. The newer Biopython releases are only in bioconda (and right now, I have no compelling reason to write new legacy XML packages for them). Likewise any Galaxy package using NCBI BLAST+ needing/wanting to work under both the legacy XML packaging system and bioconda will be able to point at BLAST+ 2.5.0. Peter On Wed, Apr 19, 2017 at 1:17 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

I've emailed the rest of the IUC for their input - adding the old versions in bioconda should work, or adding the recent Biopython releases as packages on the Tool Shed.

For blast_rbh just need a semi-recent Biopython available in both systems (until everyone moves over to bioconda - we've not yet done this on our local Galaxy for example).

Peter

Peter

On Wed, 19 Apr 2017 at 13:04, Matthias Bernt <m.bernt@ufz.de> wrote:

...

Dear Peter,

thanks. Just for understanding: Why not just change the biopython dependency from 1.67 to 1.69, if this is the one available in bioconda. blast_rbh seems to use only the SeqIO fasta parser and writer. This should be no problem.

But I guess that for older versions of blast_rbh one might still need legacy packages of biopython. Or could one change the dependencies in older versions? Or would this be no good idea because of backward compatibility?

Cheers, Matthias

On 19.04.2017 13:50, Peter Cock wrote:

...

Just lucky timing, could you try blast_rbh v0.1.11,

https://toolshed.g2.bx.psu.edu/view/peterjc/blast_rbh/d8d9a9069586

For BLAST+ this ought to work with either bioconda, or the legacy XML based packages, as both have BLAST+ 2.5.0.

However, it looks like bioconda only has Biopython 1.68 and 1.69, while the legacy XML based packages only go up to Biopython 1.67 at the time of writing... it looks like we'll need to add a couple more legacy packages.

Peter

On Wed, Apr 19, 2017 at 12:01 PM, Matthias Bernt <m.bernt@ufz.de> wrote:

...

Dear Peter,

thanks for the info. Would be great to get the update, but since I have a method that is working for the moment there is no need to hurry.

Best, Matthias

On 19.04.2017 12:57, Peter Cock wrote:

...

Oh right - I've just been updating ncbi_blast_plus this morning to transition to BLAST+ 2.5.0 via either bioconda or the older legacy Tool Shed.

I can try to update blast_rbh next, which may solve this by letting you use bioconda.

Peter

On Wed, Apr 19, 2017 at 11:52 AM, Matthias Bernt <m.bernt@ufz.de> wrote:

...

Dear Marius,

thanks again for the help. I'm trying to install blast_rbh (owner is peterjc). The dependencies look as follows:

blast_rbh - biopython - package_biopython_1_64 - package_numpy_1_8 - package_atlas_3_10 - blast - package_blast_plus_2_2_31 - blast+

With unchecked "When available, install Tool Shed managed tool dependencies?" I get all as "Installed, missing tool dependencies". Blast_rbh is not working since blast+ is not installed. Even if I install blast+ manually (in galaxy) its not working (makeblastdb is missing).

When I leave "When available, install Tool Shed managed tool dependencies?" I see blast_rbh, package_blast_plus package_biopython as installed and the others as Installed, missing tool dependencies. Here blast_rbh is working.

What would be your suggestion? Live with the latter and file an issue at the tools repository (difficult to say which causes the problem(s))?

I get similar behavior if I try to install from the test toolshed. (Only a different error from atlas: /bin/sh: line 3: /host/static_full_blas_lapack.diff: No such file or directory).

But, actually I'm trying to automatize tool installation using the ansible role ansible-galaxy-tools (https://github.com/galaxyproject/ansible-galaxy-tools). With this method I get the latter behavior. The role uses uses ephemeris==0.4.0 to install tools. There I have seen three global variables that (I guess) control the installation of dependencies.

INSTALL_TOOL_DEPENDENCIES = False INSTALL_REPOSITORY_DEPENDENCIES = True INSTALL_RESOLVER_DEPENDENCIES = True

I guess I could control the behavior with the latter two variables.

Best, Matthias

On 18.04.2017 19:24, Marius van den Beek wrote: > > > Hi Matthias, > > it's me again! > What tool are you trying to install? > > My -perhaps- unhelpful suggestion is to not install anything that > starts > with > package_* (also called tool shed packages), those should be > exclusively > installed when you absolutely need > to install an old tool that can only function with packages. > We've switched to conda nowadays, which is much easier to install > and to > maintain. > In fact the IUC has ported all their latest tools to conda, and > similarly most devteam > tools that are still in active use have also been ported to use > Conda > dependencies. > > If you look at this > document > > https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/, > there is a part where you confirm dependencies. If you click on show > detail, and you unselect > When available, install Tool Shed managed tool dependencies? > Galaxy will not try to install these old packages. There are some > tools > which come both with > old toolshed dependencies and that have Conda available. You may be > lucky and find that > the tool you are trying to install has Conda dependencies available. > There is a lot more background on the Toolshed and Conda in this > document here: > https://docs.galaxyproject.org/en/master/admin/conda_faq.html > > Best, > Marius > > On 18 April 2017 at 19:03, Matthias Bernt <m.bernt@ufz.de > <mailto:m.bernt@ufz.de>> wrote: > > Dear list, > > again me :( stumbling from problem to problem ... > > I got compilation errors when installing > > package_atlas_3_10 Revision: 98c017ec230d > > I tried with gcc 4x and 6x without success. Do I need the intel > C > compiler for this tool? > > If I got earlier posts > > > (http://dev.list.galaxyproject.org/atlas-3-10-IUC-error-tt4668236.html > > > <http://dev.list.galaxyproject.org/atlas-3-10-IUC-error-tt4668236.html>) > > correct a precompiled version should be used anyway? > > I'm running galaxy on CentOS 6.8 (64bit) (running in a > VirtualBox). > > Best, > Matthias > > > Here is the output (which I guess is verbose output from > configure): > > > /tmp/cctyMGAH.o: In function `ATL_tmpnam': > > > > /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: > warning: the use of `tmpnam' is dangerous, better use `mkstemp' > probe_OS.o: In function `ATL_tmpnam': > > > > /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: > warning: the use of `tmpnam' is dangerous, better use `mkstemp' > probe_asm.o: In function `ATL_tmpnam': > > > > /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: > warning: the use of `tmpnam' is dangerous, better use `mkstemp' > system(make IRun_GAS_x8632 args="-v 2" MYFLAGS="-DATL_OS_Linux" > 2> > /dev/null | fgrep SUCCESS) > > ierr=256 in command='make IRun_GAS_x8632 args="-v 2" > MYFLAGS="-DATL_OS_Linux" 2> /dev/null | fgrep SUCCESS'! > > OUTPUT: > ======= > system(make IRun_GAS_x8664 args="-v 2" MYFLAGS="-DATL_OS_Linux" > 2> > /dev/null | fgrep SUCCESS) > probe_vec.o: In function `ATL_tmpnam': > > > > /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: > warning: the use of `tmpnam' is dangerous, better use `mkstemp' > > ierr=256 in command='make IRun_VSX MYFLAGS='-DATL_OS_Linux > -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'! > > OUTPUT: > ======= > > ierr=256 in command='make IRun_AltiVec MYFLAGS='-DATL_OS_Linux > -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'! > > OUTPUT: > ======= > > ierr=256 in command='make IRun_AVXFMA4 MYFLAGS='-DATL_OS_Linux > -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'! > > OUTPUT: > ======= > > ierr=256 in command='make IRun_3DNow MYFLAGS='-DATL_OS_Linux > -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'! > > OUTPUT: > ======= > > ierr=256 in command='make IRun_NEON MYFLAGS='-DATL_OS_Linux > -DATL_GAS_x8664' 2> /dev/null | fgrep SUCCESS'! > > OUTPUT: > ======= > probe_arch.o: In function `ATL_tmpnam': > > > > /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: > warning: the use of `tmpnam' is dangerous, better use `mkstemp' > /tmp/cc8hbxc1.o: In function `ATL_tmpnam': > > > > /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: > warning: the use of `tmpnam' is dangerous, better use `mkstemp' > ERROR: enum fam=3, chip=2, model=79, mach=0 > make[3]: *** [atlas_run] Error 44 > make[2]: *** [IRunArchInfo_x86] Error 2 > /tmp/ccafA8Bi.o: In function `ATL_tmpnam': > > > > /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: > warning: the use of `tmpnam' is dangerous, better use `mkstemp' > ERROR: enum fam=3, chip=2, model=79, mach=0 > make[3]: *** [atlas_run] Error 44 > make[2]: *** [IRunArchInfo_x86] Error 2 > ERROR: enum fam=3, chip=2, model=79, mach=0 > make[3]: *** [atlas_run] Error 44 > make[2]: *** [IRunArchInfo_x86] Error 2 > cmnd='make IRun_comp args="-v 2 -o atlconf.txt -O 1 -A 39 -Si > nof77 > 0 -V 488 -Fa ic '-fPIC' -Fa sm '-fPIC' -Fa dm '-fPIC' -Fa sk > '-fPIC' -Fa dk '-fPIC' -Fa xc '-fPIC' -Fa gc '-fPIC' -Fa if > '-fPIC' > -b 64"' > /tmp/cc8W8Itx.o: In function `ATL_tmpnam': > > > > /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: > warning: the use of `tmpnam' is dangerous, better use `mkstemp' > probe_comp.o: In function `ATL_tmpnam': > > > > /gpfs1/data/galaxy_server/galaxy-dev/database/tmp/tmp-toolshed-mtdAAKCLe/ATLAS/build/..//CONFIG/include/atlas_sys.h:224: > warning: the use of `tmpnam' is dangerous, better use `mkstemp' > > ierr=256 in command='find > /gpfs1/data/galaxy_server/galaxy-dev/.venv/bin > /usr/local/gcc/6.2.0-1/bin > /global/apps/bioinf/galaxy/bin/Python-2.7.13/bin > /usr/local/sqlite/3.15.1-1/bin > /global/apps/bioinf/galaxy/bin/postgresql-9.6.2/bin > /usr/local/git/2.10.1-1/bin /usr/local/pcre/8.38-1/bin > /usr/local/ncurses/5.9-1/bin /usr/local/bzip2/1.0.6-3/bin > /usr/local/expat/2.1.1-1/bin /usr/local/curl/7.41.0-1/bin > /usr/local/openssl/1.0.2-1/usr/bin > /usr/local/uge/8.4.4-1/bin/lx-amd64 /usr/local/bin /bin /usr/bin > /usr/local/sbin /usr/sbin /sbin /home/songalax/bin -maxdepth 1 > -name > '*gcc*' -exec ./xisgcc '{}' \;'! > > OUTPUT: > ======= > cmnd=make IRunCComp CC='/usr/local/gcc/6.2.0-1/bin/gcc' > CCFLAGS='-O' | fgrep SUCCESS > /usr/local/gcc/6.2.0-1/bin/gcc -O : SUCCESS! > cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O' | fgrep > SUCCESS > /usr/bin/gcc -O : SUCCESS! > sh: -c: line 0: unexpected EOF while looking for matching ``' > sh: -c: line 1: syntax error: unexpected end of file > > ierr=256 in command='find $HOME/local -name '*gcc*' -exec > ./xisgcc > '{}' \;'! > > OUTPUT: > ======= > cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O' | fgrep > SUCCESS > /usr/bin/gcc -O : SUCCESS! > sh: -c: line 0: unexpected EOF while looking for matching ``' > sh: -c: line 1: syntax error: unexpected end of file > > ierr=256 in command='find /usr/local /bin /sbin /usr/bin > /usr/sbin > /opt/bin /opt/sbin -name '*gcc*' -exec ./xisgcc '{}' \;'! > > OUTPUT: > ======= > cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O' | fgrep > SUCCESS > /usr/bin/gcc -O : SUCCESS! > sh: -c: line 0: unexpected EOF while looking for matching ``' > sh: -c: line 1: syntax error: unexpected end of file > sh: -c: line 0: unexpected EOF while looking for matching ``' > sh: -c: line 1: syntax error: unexpected end of file > > Compiler nodes: Fresh Read > 0. priority=0, comps,OS,arch[0]=(128,1,1), comp='f77' > '-O' > 1. priority=4, comps,OS,arch[0]=(128,1,1), comp='g77' > '-O' > 2. priority=5, comps,OS,arch[0]=(128,1,1), comp='gfortran' > '-O' > 3. priority=5, comps,OS,arch[0]=(127,1,1), comp='gcc' > '-O -fomit-frame-pointer' > 4. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran' > '-mcpu=cortex-a8 -mfpu=vfpv3 -mfloat-abi=softfp -O' > 5. priority=1000, comps,OS,arch[0]=(20,1,0), comp='gcc' > '-O1 -mcpu=cortex-a8 -mtune=cortex-a8 -mfpu=vfpv3 > -mfloat-abi=softfp -fno-schedule-insns2' > 6. priority=1000, comps,OS,arch[0]=(75,1,0), comp='gcc' > '-O1 -mcpu=cortex-a8 -mtune=cortex-a8 -mfpu=vfpv3 > -mfloat-abi=softfp -fno-expensive-optimizations' > 7. priority=1000, comps,OS,arch[0]=(32,1,0), comp='gcc' > '-mcpu=cortex-a8 -O1 -mfpu=vfpv3 -mfloat-abi=softfp ' > 8. priority=0, comps,OS,arch[0]=(63,768,1075838976), > comp='icl' > '-QxN -O3 -Qprec -fp:extended -fp:except -nologo -Oy' > 9. priority=0, comps,OS,arch[0]=(128,768,1), comp='ifort' > '-O2 -fltconsistency -nologo' > 10. priority=0, comps,OS,arch[0]=(63,768,1), comp='cl' > '-Oy -Ox -arch:SSE2 -nologo' > 11. priority=4, comps,OS,arch[0]=(63,768,1048576), comp='cl' > '-Oy -Ox -arch:SSE -nologo' > 12. priority=4, comps,OS,arch[0]=(63,768,983040), comp='cl' > '-Oy -Ox' > 13. priority=500, comps,OS,arch[0]=(127,1,3584), comp='gcc' > '-O3 -funroll-loops' > 14. priority=500, comps,OS,arch[0]=(128,1,3584), > comp='gfortran' > '-O3 -funroll-loops' > 15. priority=600, comps,OS,arch[0]=(128,1,2048), > comp='gfortran' > '-march=z9-109 -O3 -funroll-loops' > 16. priority=600, comps,OS,arch[0]=(127,1,2048), comp='gcc' > '-march=z9-109 -O3 -funroll-loops' > 17. priority=800, comps,OS,arch[0]=(128,1,2048), > comp='gfortran' > '-march=z10 -O3 -funroll-loops -fno-prefetch-loop-arrays' > 18. priority=800, comps,OS,arch[0]=(127,1,2048), comp='gcc' > '-march=z10 -O3 -funroll-loops -fno-prefetch-loop-arrays' > 19. priority=1000, comps,OS,arch[0]=(127,1,2048), comp='gcc' > '-march=z196 -O3 -funroll-loops -fno-prefetch-loop-arrays' > 20. priority=1000, comps,OS,arch[0]=(128,1,2048), > comp='gfortran' > '-march=z196 -O3 -funroll-loops -fno-prefetch-loop-arrays' > 21. priority=600, comps,OS,arch[0]=(127,1,1024), comp='gcc' > '-march=z9-109 -O3 -funroll-loops > -fno-prefetch-loop-arrays' > 22. priority=600, comps,OS,arch[0]=(128,1,1024), > comp='gfortran' > '-march=z9-109 -O3 -funroll-loops' > 23. priority=1000, comps,OS,arch[0]=(127,1,1024), comp='gcc' > '-march=z10 -O3 -funroll-loops -fno-prefetch-loop-arrays' > 24. priority=1000, comps,OS,arch[0]=(127,1,512), comp='gcc' > '-march=z9-109 -O3 -funroll-loops' > 25. priority=1010, comps,OS,arch[0]=(128,1,4), comp='xlf' > '-qtune=pwr4 -qarch=pwr4 -O3 -qmaxmem=-1 -qfloat=hsflt' > 26. priority=1010, comps,OS,arch[0]=(127,1,4), comp='gcc' > '-mcpu=power4 -mtune=power4 -O3 -fno-schedule-insns > -fno-rerun-loop-opt' > 27. priority=1010, comps,OS,arch[0]=(128,1,8), comp='xlf' > '-qtune=pwr5 -qarch=pwr5 -O3 -qmaxmem=-1 -qfloat=hsflt' > 28. priority=1010, comps,OS,arch[0]=(128,1,128), comp='xlf' > '-qtune=pwr7 -qarch=pwr7 -O3 -qmaxmem=-1 -qfloat=hsflt' > 29. priority=1010, comps,OS,arch[0]=(128,1,8), comp='gfortran' > '-mcpu=power5 -mtune=power5 -O3 -fno-schedule-insns > -fno-rerun-loop-opt' > 30. priority=1010, comps,OS,arch[0]=(128,1,64), comp='gfortran' > '-mcpu=power6 -mtune=power6 -maltivec -O3 > -fno-schedule-insns > -fschedule-insns2 -minsert-sched-nops=2' > 31. priority=1010, comps,OS,arch[0]=(127,1,8), comp='gcc' > '-mcpu=power5 -mtune=power5 -O3 -fno-schedule-insns > -fno-rerun-loop-opt' > 32. priority=1010, comps,OS,arch[0]=(127,1,64), comp='gcc' > '-mcpu=power6 -mtune=power6 -maltivec -O3 > -fno-schedule-insns > -fschedule-insns2 -minsert-sched-nops=2' > 33. priority=1010, comps,OS,arch[0]=(128,1,128), > comp='gfortran' > '-O2 -mvsx -mcpu=power7 -mtune=power7 -m64 -mvrsave > -funroll-all-loops' > 34. priority=1010, comps,OS,arch[0]=(127,1,128), comp='gcc' > '-O2 -mvsx -mcpu=power7 -mtune=power7 -m64 -mvrsave > -funroll-all-loops' > 35. priority=1000, comps,OS,arch[0]=(8,1,32), comp='gcc' > '-mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970 > -O2 > -mvrsave' > 36. priority=1000, comps,OS,arch[0]=(117,1,32), comp='gcc' > '-mpowerpc64 -maltivec -mabi=altivec -mcpu=970 -mtune=970 > -O2' > 37. priority=1000, comps,OS,arch[0]=(2,1,32), comp='gcc' > '-Os -mpowerpc64 -maltivec -mabi=altivec -mcpu=970 > -mtune=970 > -mvrsave -fno-schedule-insns2 -fno-schedule-insns' > 38. priority=1000, comps,OS,arch[0]=(121,1,16), comp='gcc' > '-O3 -maltivec -mabi=altivec -mcpu=7400 -mtune=7400 > -fno-schedule-insns -fschedule-insns2' > 39. priority=1000, comps,OS,arch[0]=(2,1,16), comp='gcc' > '-Os -maltivec -mabi=altivec -mcpu=7400 -mtune=7400' > 40. priority=1000, comps,OS,arch[0]=(4,1,16), comp='gcc' > '-Os -maltivec -mabi=altivec -mcpu=7400 -mtune=7400' > 41. priority=1, comps,OS,arch[0]=(33,1,0), comp='pathcc' > '-march=auto -O2 -OPT:Olimit=15000 -LNO:blocking=OFF' > 42. priority=1, comps,OS,arch[0]=(6,1,0), comp='pathcc' > '-O3 -OPT:Olimit=15000 -LNO:blocking=OFF -LOPT:alias=typed > -march=auto -LNO:opt=0 -LNO:full_unroll_outer=OFF -LNO:fusion=0 > -LNO:prefetch=2' > 43. priority=1, comps,OS,arch[0]=(24,1,0), comp='pathcc' > '-O3 -OPT:Olimit=15000 -LNO:blocking=OFF -LOPT:alias=typed > -march=auto' > 44. priority=1000, comps,OS,arch[0]=(128,1,0), comp='pathf95' > '-march=auto -O2' > 45. priority=500, comps,OS,arch[0]=(127,1,0), comp='gcc' > '-O2 -mips64 -march=5kf -mtune=5kf -fno-schedule-insns > -fschedule-insns2 -fno-peephole -fno-peephole2' > 46. priority=1000, comps,OS,arch[0]=(128,32,0), comp='f77' > '-O2' > 47. priority=1000, comps,OS,arch[0]=(97,32,0), comp='cc' > '-O2 -OPT:Olimit=15000 -LNO:blocking=OFF' > 48. priority=1000, comps,OS,arch[0]=(30,32,0), comp='cc' > '-O3 -OPT:Olimit=15000 -LNO:blocking=OFF -LOPT:alias=typed' > 49. priority=1010, comps,OS,arch[0]=(128,1,0), comp='gfortran' > '-fomit-frame-pointer -O2 -fno-tree-loop-optimize' > 50. priority=1000, comps,OS,arch[0]=(30,1,0), comp='gcc' > '-fomit-frame-pointer -O2' > 51. priority=1010, comps,OS,arch[0]=(30,1,0), comp='gcc' > '-fomit-frame-pointer -O2 -fno-tree-loop-optimize' > 52. priority=10, comps,OS,arch[0]=(128,1,0), comp='g77' > '-O -mcpu=ultrasparc3 -mtune=ultrasparc3' > 53. priority=100, comps,OS,arch[0]=(128,1,0), comp='gfortran' > '-O -mcpu=ultrasparc3 -mtune=ultrasparc3' > 54. priority=1000, comps,OS,arch[0]=(128,1,0), comp='f77' > '-dalign -native -xO5' > 55. priority=1000, comps,OS,arch[0]=(96,1,0), comp='gcc' > '-mcpu=ultrasparc3 -mtune=ultrasparc3 -O' > 56. priority=1000, comps,OS,arch[0]=(29,1,0), comp='gcc' > '-O3 -mcpu=ultrasparc3 -mtune=ultrasparc3 > -fno-schedule-insns2 > -fschedule-insns' > 57. priority=1000, comps,OS,arch[0]=(2,1,0), comp='gcc' > '-O1 -mcpu=ultrasparc3 -mtune=ultrasparc3 -fschedule-insns > -fmodulo-sched' > 58. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran' > '-mcpu=niagara2 -mtune=niagara2 -Os' > 59. priority=1000, comps,OS,arch[0]=(127,1,0), comp='gcc' > '-mcpu=niagara2 -mtune=niagara2 -Os' > 60. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc' > '-fomit-frame-pointer -mfpmath=sse -mfma4 -O2 > -fno-tree-loop-optimize' > 61. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc' > '-Os -fomit-frame-pointer' > 62. priority=1005, comps,OS,arch[0]=(95,896,0), comp='gcc' > '-fomit-frame-pointer -mfpmath=sse -O2' > 63. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc' > '-fomit-frame-pointer -mfpmath=sse -O2' > 64. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran' > '-fomit-frame-pointer -mfpmath=sse -O2' > 65. priority=1000, comps,OS,arch[0]=(95,1,12582912), comp='gcc' > '-fomit-frame-pointer -O3 -mfpmath=387' > 66. priority=1005, comps,OS,arch[0]=(31,896,12582912), > comp='gcc-4' > '-fomit-frame-pointer -O3 -mfpmath=387' > 67. priority=1000, comps,OS,arch[0]=(95,1,-1071906816), > comp='gcc' > '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' > 68. priority=1005, comps,OS,arch[0]=(31,896,1835008), > comp='gcc-4' > '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' > 69. priority=1000, comps,OS,arch[0]=(128,1,1835008), > comp='gfortran' > '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' > 70. priority=1000, comps,OS,arch[0]=(95,1,0), comp='gcc' > '-fomit-frame-pointer -mfpmath=387 -O2' > 71. priority=1005, comps,OS,arch[0]=(31,896,0), comp='gcc-4' > '-fomit-frame-pointer -mfpmath=387 -O2' > 72. priority=1000, comps,OS,arch[0]=(128,1,0), comp='gfortran' > '-fomit-frame-pointer -mfpmath=387 -O2' > 73. priority=1000, comps,OS,arch[0]=(25,1,-1073741824), > comp='gcc-4' > '-O2 -fomit-frame-pointer -mfpmath=sse' > 74. priority=1005, comps,OS,arch[0]=(6,896,-1073741824), > comp='gcc-4' > '-O2 -fomit-frame-pointer -mfpmath=sse -fno-schedule-insns > -fno-optimize-register-move' > 75. priority=1000, comps,OS,arch[0]=(6,1,-1073741824), > comp='gcc' > '-O2 -fomit-frame-pointer -mfpmath=sse -fno-schedule-insns > -fno-optimize-register-move' > 76. priority=1000, comps,OS,arch[0]=(25,1,-2147483648), > comp='gcc' > '-O2 -fomit-frame-pointer -mfpmath=sse' > 77. priority=1000, comps,OS,arch[0]=(128,1,-1073741824), > comp='gfortran' > '-O2 -fomit-frame-pointer -mfpmath=sse' > 78. priority=1000, comps,OS,arch[0]=(128,1,32768), > comp='gfortran' > '-fomit-frame-pointer -mfpmath=sse -O2' > 79. priority=1000, comps,OS,arch[0]=(95,1,32768), comp='gcc' > '-fomit-frame-pointer -mfpmath=sse -O2' > 80. priority=1000, comps,OS,arch[0]=(128,1,16384), > comp='gfortran' > '-fomit-frame-pointer -mfpmath=sse -O2' > 81. priority=1000, comps,OS,arch[0]=(95,1,16384), comp='gcc' > '-fomit-frame-pointer -mfpmath=sse -O2' > 82. priority=1000, comps,OS,arch[0]=(128,1,8192), > comp='gfortran' > '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' > 83. priority=1000, comps,OS,arch[0]=(10,1,8192), comp='gcc' > '-fomit-frame-pointer -mfpmath=sse -O2' > 84. priority=1000, comps,OS,arch[0]=(85,1,8192), comp='gcc' > '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' > 85. priority=1000, comps,OS,arch[0]=(128,1,12288), > comp='gfortran' > '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' > 86. priority=1000, comps,OS,arch[0]=(95,1,4096), comp='gcc' > '-fomit-frame-pointer -mfpmath=387 -O2 -falign-loops=4' > 87. priority=1000, comps,OS,arch[0]=(65,1,536870912), > comp='gcc' > '-O' > 88. priority=1000, comps,OS,arch[0]=(30,1,536870912), > comp='gcc' > '-O3 -fno-schedule-insns2 -funroll-all-loops -fno-tree-ch' > 89. priority=1000, comps,OS,arch[0]=(95,1,33554432), comp='gcc' > '-fomit-frame-pointer -mfpmath=sse -O2' > 90. priority=1005, comps,OS,arch[0]=(31,896,33554432), > comp='gcc-4' > '-fomit-frame-pointer -mfpmath=sse -O2' > 91. priority=1000, comps,OS,arch[0]=(95,1,67108864), comp='gcc' > '-fomit-frame-pointer -mfpmath=sse -O2 > -fno-schedule-insns2' > 92. priority=1005, comps,OS,arch[0]=(95,896,67108864), > comp='gcc-4' > '-fomit-frame-pointer -mfpmath=sse -O2 > -fno-schedule-insns2' > 93. priority=50, comps,OS,arch[0]=(57,1,134217728), > comp='clang' > '-fomit-frame-pointer -mavx -O2 -m64 -Wno-parentheses' > 94. priority=1000, comps,OS,arch[0]=(127,1,134217728), > comp='gcc' > '-fomit-frame-pointer -mfpmath=sse -O2 > -fno-schedule-insns2' > 95. priority=1005, comps,OS,arch[0]=(31,896,134217728), > comp='gcc-4' > '-fomit-frame-pointer -mfpmath=sse -O2 > -fno-schedule-insns2' > 96. priority=1000, comps,OS,arch[0]=(127,1,268435456), > comp='gcc' > '-fomit-frame-pointer -mfpmath=sse -O2' > > > Compiler nodes: Targeted > 0. priority=0, comps,OS,arch[0]=(128,1,1), comp='f77' > '-O' > 1. priority=4, comps,OS,arch[0]=(128,1,1), comp='g77' > '-O' > 2. priority=5, comps,OS,arch[0]=(128,1,1), comp='gfortran' > '-O' > 3. priority=5, comps,OS,arch[0]=(127,1,1), comp='gcc' > '-O -fomit-frame-pointer' > > > Compiler nodes: Sorted > 0. priority=0, comps,OS,arch[0]=(128,1,1), comp='f77' > '-O' > 1. priority=4, comps,OS,arch[0]=(128,1,1), comp='g77' > '-O' > 2. priority=5, comps,OS,arch[0]=(127,1,1), comp='gcc' > '-O -fomit-frame-pointer' > 3. priority=5, comps,OS,arch[0]=(128,1,1), comp='gfortran' > '-O' > > cc1: error: unrecognized command line option "-mavx2" > make[2]: *** [IRunCComp] Error 1 > > ierr=256 in command='make IRunCComp CC='/usr/bin/gcc' > CCFLAGS='-O > -fomit-frame-pointer -mavx2 -mfma -fPIC -m64' | fgrep SUCCESS'! > > OUTPUT: > ======= > cmnd=make IRunCComp CC='/usr/bin/gcc' CCFLAGS='-O > -fomit-frame-pointer -mavx2 -mfma -fPIC -m64' | fgrep SUCCESS > /usr/bin/gcc -O -fomit-frame-pointer -mavx2 -mfma -fPIC -m64 > : > FAILURE! > > > Unable to find usable compiler for ICC; abortingMake sure > compilers > are in your path, and specify good compilers to configure > (see INSTALL.txt or 'configure --help' for details)make[1]: *** > [atlas_run] Error 1 > make: *** [IRun_comp] Error 2 > ERROR 512 IN SYSCMND: 'make IRun_comp args="-v 2 -o atlconf.txt > -O 1 > -A 39 -Si nof77 0 -V 488 -Fa ic '-fPIC' -Fa sm '-fPIC' -Fa dm > '-fPIC' -Fa sk '-fPIC' -Fa dk '-fPIC' -Fa xc '-fPIC' -Fa gc > '-fPIC' > -Fa if '-fPIC' -b 64"' > Make.top:1: Make.inc: No such file or directory > Make.top:329: warning: overriding commands for target > `/AtlasTest' > Make.top:80: warning: ignoring old commands for target > `/AtlasTest' > make[1]: *** No rule to make target `Make.inc'. Stop. > make: *** [startup] Error 2 > mv: cannot stat `lib/Makefile': No such file or directory > ../configure: line 450: lib/Makefile: No such file or directory > ../configure: line 451: lib/Makefile: No such file or directory > ../configure: line 452: lib/Makefile: No such file or directory > ../configure: line 453: lib/Makefile: No such file or directory > ../configure: line 509: lib/Makefile: No such file or directory > Make.top:1: Make.inc: No such file or directory > Make.top:329: warning: overriding commands for target > `/AtlasTest' > Make.top:80: warning: ignoring old commands for target > `/AtlasTest' > make[1]: *** No rule to make target `Make.inc'. Stop. > make: *** [build] Error 2 > -- > > ------------------------------------------- > Matthias Bernt > Bioinformatics Service > Molekulare Systembiologie (MOLSYB) > Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ > Helmholtz Centre for Environmental Research GmbH - UFZ > Permoserstraße 15, 04318 Leipzig, Germany > Phone +49 341 235 482296 <tel:%2B49%20341%20235%20482296>, > m.bernt@ufz.de <mailto:m.bernt@ufz.de>, www.ufz.de > <http://www.ufz.de> > > Sitz der Gesellschaft/Registered Office: Leipzig > Registergericht/Registration Office: Amtsgericht Leipzig > Handelsregister Nr./Trade Register Nr.: B 4703 > Vorsitzender des Aufsichtsrats/Chairman of the Supervisory > Board: > MinDirig Wilfried Kraus > Wissenschaftlicher Geschäftsführer/Scientific Managing Director: > Prof. Dr. Dr. h.c. Georg Teutsch > Administrative Geschäftsführerin/ Administrative Managing > Director: > Prof. Dr. Heike Graßmann > ------------------------------------------- > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > https://lists.galaxyproject.org/ > <https://lists.galaxyproject.org/> > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ > <http://galaxyproject.org/search/> > >

--

------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/

--

------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------

--

------------------------------------------- Matthias Bernt Bioinformatics Service Molekulare Systembiologie (MOLSYB) Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482296, m.bernt@ufz.de, www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Dr. h.c. Georg Teutsch Administrative Geschäftsführerin/ Administrative Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------